NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|521257151|ref|WP_020443716|]
View 

3-isopropylmalate dehydratase small subunit [Psychrobacter sp. G]

Protein Classification

3-isopropylmalate dehydratase small subunit( domain architecture ID 10011702)

3-isopropylmalate dehydratase small subunit catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate

CATH:  3.20.19.10
EC:  4.2.1.33
Gene Symbol:  leuD
Gene Ontology:  GO:0003861|GO:0009098
PubMed:  20938981
SCOP:  4003492

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
leuD PRK01641
3-isopropylmalate dehydratase small subunit;
1-210 8.69e-141

3-isopropylmalate dehydratase small subunit;


:

Pssm-ID: 179314 [Multi-domain]  Cd Length: 200  Bit Score: 391.41  E-value: 8.69e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   1 MQAYNTQKGIVCPLDRANVDTDQIIAKQFLKSIKRTGFGVNLFDDWRYLDEGYPgqdnstriiNPDFILNKPRYQGASIL 80
Cdd:PRK01641   1 MEKFTTHTGLAVPLDRANVDTDQIIPKQFLKRITRTGFGKGLFDDWRYLDDGQP---------NPDFVLNQPRYQGASIL 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  81 LARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTLMKATFANEGYELTADLERQVVI 160
Cdd:PRK01641  72 LAGDNFGCGSSREHAPWALADYGFRAVIAPSFADIFYNNCFKNGLLPIVLPEEDVDELFKLVEANPGAELTVDLEAQTVT 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 521257151 161 TPtGEEYAFEVDDFRKHCLLNGLDDIGLTLQQSDAIKEYEHKMMQKTPWI 210
Cdd:PRK01641 152 AP-DKTFPFEIDPFRRHCLLNGLDDIGLTLQHEDAIAAYEAKRPAFRPWL 200
 
Name Accession Description Interval E-value
leuD PRK01641
3-isopropylmalate dehydratase small subunit;
1-210 8.69e-141

3-isopropylmalate dehydratase small subunit;


Pssm-ID: 179314 [Multi-domain]  Cd Length: 200  Bit Score: 391.41  E-value: 8.69e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   1 MQAYNTQKGIVCPLDRANVDTDQIIAKQFLKSIKRTGFGVNLFDDWRYLDEGYPgqdnstriiNPDFILNKPRYQGASIL 80
Cdd:PRK01641   1 MEKFTTHTGLAVPLDRANVDTDQIIPKQFLKRITRTGFGKGLFDDWRYLDDGQP---------NPDFVLNQPRYQGASIL 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  81 LARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTLMKATFANEGYELTADLERQVVI 160
Cdd:PRK01641  72 LAGDNFGCGSSREHAPWALADYGFRAVIAPSFADIFYNNCFKNGLLPIVLPEEDVDELFKLVEANPGAELTVDLEAQTVT 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 521257151 161 TPtGEEYAFEVDDFRKHCLLNGLDDIGLTLQQSDAIKEYEHKMMQKTPWI 210
Cdd:PRK01641 152 AP-DKTFPFEIDPFRRHCLLNGLDDIGLTLQHEDAIAAYEAKRPAFRPWL 200
LeuD COG0066
3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism]; ...
 2-202 1.12e-121

3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism]; 3-isopropylmalate dehydratase small subunit is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis


Pssm-ID: 439836 [Multi-domain]  Cd Length: 195  Bit Score: 342.92  E-value: 1.12e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   2 QAYNTQKGIVCPLDRANVDTDQIIAKQFLKSIKRTGFGVNLFDDWRYLDEgypgqdnstriINPDFILNKPRYQGASILL 81
Cdd:COG0066    1 EKFTTLTGRAVPLDGDNIDTDQIIPARFLKTIDREGLGKHLFEDWRYDRS-----------PDPDFVLNQPRYQGADILV 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  82 ARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTLMKATFANEGYELTADLERQVVIT 161
Cdd:COG0066   70 AGRNFGCGSSREHAPWALKDYGFRAVIAPSFADIFYRNAINNGLLPIELPEEAVDALFAAIEANPGDELTVDLEAGTVTN 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 521257151 162 PTGEEYAFEVDDFRKHCLLNGLDDIGLTLQQSDAIKEYEHK 202
Cdd:COG0066  150 GTGETYPFEIDPFRRECLLNGLDDIGLTLKHADAIAAFEAK 190
leuD TIGR00171
3-isopropylmalate dehydratase, small subunit; Homoaconitase, aconitase, and 3-isopropylmalate ...
 1-196 4.53e-97

3-isopropylmalate dehydratase, small subunit; Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. The candidate archaeal leuD proteins are not included in the seed alignment for this model and score below the trusted cutoff. [Amino acid biosynthesis, Pyruvate family]


Pssm-ID: 129275 [Multi-domain]  Cd Length: 188  Bit Score: 280.55  E-value: 4.53e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151    1 MQAYNTQKGIVCPLDRANVDTDQIIAKQFLKSIKRTGFGVNLFDDWRYLDEGypGQDNstriiNPDFILNKPRYQGASIL 80
Cdd:TIGR00171   1 MAPFKSHTGLVAPLDAANVDTDAIIPKQFLKRITRTGFGKHLFFDWRFLDAN--GKEP-----NPDFVLNQPQYQGASIL 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   81 LARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTLMkATFANEGYELTADLERQVVI 160
Cdd:TIGR00171  74 LARENFGCGSSREHAPWALDDYGFKVIIAPSFADIFYNNSFKNGLLPIRLSYDEVKELF-GQVENQGLQMTVDLENQLIH 152

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 521257151  161 TPTGEEYAFEVDDFRKHCLLNGLDDIGLTLQQSDAI 196
Cdd:TIGR00171 153 DSEGKVYSFEIDPFRKHCLINGLDEIGLTLQHEDEI 188
Aconitase_C pfam00694
Aconitase C-terminal domain; Members of this family usually also match to pfam00330. This ...
 1-133 7.21e-48

Aconitase C-terminal domain; Members of this family usually also match to pfam00330. This domain undergoes conformational change in the enzyme mechanism.


Pssm-ID: 459908 [Multi-domain]  Cd Length: 131  Bit Score: 153.68  E-value: 7.21e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151    1 MQAYNTQKGIVCPLDRANVDTDQIIAKQFLKSIKRTGFGVNLFDDWRYL-DEGYPGQDNstriinPDFILNKPRYQ--GA 77
Cdd:pfam00694   1 MPVFLKLKGKTTPDFNSNVDTDLIIPKQFLGTIANIGIGNINFEGWRYGkVRYLPDGEN------PDFYDAAMRYKqhGA 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 521257151   78 SILLAR-RNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEE 133
Cdd:pfam00694  75 PIVVIGgKNFGCGSSREHAAWALRDLGIKAVIAESFARIHRNNLIKNGLLPLEFPEE 131
IPMI_Swivel cd01577
Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized ...
 14-154 5.80e-43

Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.


Pssm-ID: 238809 [Multi-domain]  Cd Length: 91  Bit Score: 139.65  E-value: 5.80e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  14 LDRANVDTDQIIAKQFLksikrtgfgvnlfddwryldegypgqdnstriinpdfilnkpryqgASILLARRNFGCGSSRE 93
Cdd:cd01577    1 LFGDNIDTDQIIPARFL----------------------------------------------GDIIVAGKNFGCGSSRE 34

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 521257151  94 HAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTlmkaTFANEGYELTADL 154
Cdd:cd01577   35 HAPWALKDAGIRAVIAESFARIFFRNAINNGLLPVTLADEDVEE----VEAKPGDEVEVDL 91
HacB2_Meth NF040625
homoaconitase small subunit;
16-188 2.84e-21

homoaconitase small subunit;


Pssm-ID: 468597 [Multi-domain]  Cd Length: 161  Bit Score: 86.30  E-value: 2.84e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  16 RANVDTDQIIAKQFLKSIkrtgfgvNLFDDWRYLDEGypgqdnstriINPDFILNkprYQGASILLARRNFGCGSSREHA 95
Cdd:NF040625  12 GDNIDTDVIIPGRYLRTF-------NPDDLASHVMEG----------ERPDFTKN---VQKGDIIVAGWNFGCGSSREQA 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  96 PWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEivdtlmkatfANEGYELTADLERQVVIT-PTGEEYAFE-VDD 173
Cdd:NF040625  72 PVAIKHAGVSAIIAKSFARIFYRNAINIGLPVIVADIE----------ADDGDILSIDLEKGIIKNkTTGEEFKIQpFKE 141

                        170
                 ....*....|....*
gi 521257151 174 FrkhcLLNGLDDIGL 188
Cdd:NF040625 142 F----MLEILEDGGL 152
 
Name Accession Description Interval E-value
leuD PRK01641
3-isopropylmalate dehydratase small subunit;
1-210 8.69e-141

3-isopropylmalate dehydratase small subunit;


Pssm-ID: 179314 [Multi-domain]  Cd Length: 200  Bit Score: 391.41  E-value: 8.69e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   1 MQAYNTQKGIVCPLDRANVDTDQIIAKQFLKSIKRTGFGVNLFDDWRYLDEGYPgqdnstriiNPDFILNKPRYQGASIL 80
Cdd:PRK01641   1 MEKFTTHTGLAVPLDRANVDTDQIIPKQFLKRITRTGFGKGLFDDWRYLDDGQP---------NPDFVLNQPRYQGASIL 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  81 LARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTLMKATFANEGYELTADLERQVVI 160
Cdd:PRK01641  72 LAGDNFGCGSSREHAPWALADYGFRAVIAPSFADIFYNNCFKNGLLPIVLPEEDVDELFKLVEANPGAELTVDLEAQTVT 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 521257151 161 TPtGEEYAFEVDDFRKHCLLNGLDDIGLTLQQSDAIKEYEHKMMQKTPWI 210
Cdd:PRK01641 152 AP-DKTFPFEIDPFRRHCLLNGLDDIGLTLQHEDAIAAYEAKRPAFRPWL 200
LeuD COG0066
3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism]; ...
 2-202 1.12e-121

3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism]; 3-isopropylmalate dehydratase small subunit is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis


Pssm-ID: 439836 [Multi-domain]  Cd Length: 195  Bit Score: 342.92  E-value: 1.12e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   2 QAYNTQKGIVCPLDRANVDTDQIIAKQFLKSIKRTGFGVNLFDDWRYLDEgypgqdnstriINPDFILNKPRYQGASILL 81
Cdd:COG0066    1 EKFTTLTGRAVPLDGDNIDTDQIIPARFLKTIDREGLGKHLFEDWRYDRS-----------PDPDFVLNQPRYQGADILV 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  82 ARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTLMKATFANEGYELTADLERQVVIT 161
Cdd:COG0066   70 AGRNFGCGSSREHAPWALKDYGFRAVIAPSFADIFYRNAINNGLLPIELPEEAVDALFAAIEANPGDELTVDLEAGTVTN 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 521257151 162 PTGEEYAFEVDDFRKHCLLNGLDDIGLTLQQSDAIKEYEHK 202
Cdd:COG0066  150 GTGETYPFEIDPFRRECLLNGLDDIGLTLKHADAIAAFEAK 190
leuD TIGR00171
3-isopropylmalate dehydratase, small subunit; Homoaconitase, aconitase, and 3-isopropylmalate ...
 1-196 4.53e-97

3-isopropylmalate dehydratase, small subunit; Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. The candidate archaeal leuD proteins are not included in the seed alignment for this model and score below the trusted cutoff. [Amino acid biosynthesis, Pyruvate family]


Pssm-ID: 129275 [Multi-domain]  Cd Length: 188  Bit Score: 280.55  E-value: 4.53e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151    1 MQAYNTQKGIVCPLDRANVDTDQIIAKQFLKSIKRTGFGVNLFDDWRYLDEGypGQDNstriiNPDFILNKPRYQGASIL 80
Cdd:TIGR00171   1 MAPFKSHTGLVAPLDAANVDTDAIIPKQFLKRITRTGFGKHLFFDWRFLDAN--GKEP-----NPDFVLNQPQYQGASIL 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   81 LARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTLMkATFANEGYELTADLERQVVI 160
Cdd:TIGR00171  74 LARENFGCGSSREHAPWALDDYGFKVIIAPSFADIFYNNSFKNGLLPIRLSYDEVKELF-GQVENQGLQMTVDLENQLIH 152

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 521257151  161 TPTGEEYAFEVDDFRKHCLLNGLDDIGLTLQQSDAI 196
Cdd:TIGR00171 153 DSEGKVYSFEIDPFRKHCLINGLDEIGLTLQHEDEI 188
Aconitase_C pfam00694
Aconitase C-terminal domain; Members of this family usually also match to pfam00330. This ...
 1-133 7.21e-48

Aconitase C-terminal domain; Members of this family usually also match to pfam00330. This domain undergoes conformational change in the enzyme mechanism.


Pssm-ID: 459908 [Multi-domain]  Cd Length: 131  Bit Score: 153.68  E-value: 7.21e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151    1 MQAYNTQKGIVCPLDRANVDTDQIIAKQFLKSIKRTGFGVNLFDDWRYL-DEGYPGQDNstriinPDFILNKPRYQ--GA 77
Cdd:pfam00694   1 MPVFLKLKGKTTPDFNSNVDTDLIIPKQFLGTIANIGIGNINFEGWRYGkVRYLPDGEN------PDFYDAAMRYKqhGA 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 521257151   78 SILLAR-RNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEE 133
Cdd:pfam00694  75 PIVVIGgKNFGCGSSREHAAWALRDLGIKAVIAESFARIHRNNLIKNGLLPLEFPEE 131
IPMI_Swivel cd01577
Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized ...
 14-154 5.80e-43

Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.


Pssm-ID: 238809 [Multi-domain]  Cd Length: 91  Bit Score: 139.65  E-value: 5.80e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  14 LDRANVDTDQIIAKQFLksikrtgfgvnlfddwryldegypgqdnstriinpdfilnkpryqgASILLARRNFGCGSSRE 93
Cdd:cd01577    1 LFGDNIDTDQIIPARFL----------------------------------------------GDIIVAGKNFGCGSSRE 34

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 521257151  94 HAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTlmkaTFANEGYELTADL 154
Cdd:cd01577   35 HAPWALKDAGIRAVIAESFARIFFRNAINNGLLPVTLADEDVEE----VEAKPGDEVEVDL 91
PRK14812 PRK14812
hypothetical protein; Provisional
 89-202 3.45e-33

hypothetical protein; Provisional


Pssm-ID: 173273 [Multi-domain]  Cd Length: 119  Bit Score: 115.59  E-value: 3.45e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  89 GSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVDTLMKATFANegyELTADLERQVVITPTgEEYA 168
Cdd:PRK14812   3 GSSREHAAWALADYGFKVVIAGSFGDIHYNNELNNGMLPIVQPREVREKLAQLKPTD---QVTVDLEQQKIISPV-EEFT 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 521257151 169 FEVDDFRKHCLLNGLDDIGLTLQQSDAIKEYEHK 202
Cdd:PRK14812  79 FEIDSEWKHKLLNSLDDIGITLQYEELIAAYEKQ 112
leuD PRK00439
3-isopropylmalate dehydratase small subunit; Reviewed
 18-174 7.51e-28

3-isopropylmalate dehydratase small subunit; Reviewed


Pssm-ID: 234762 [Multi-domain]  Cd Length: 163  Bit Score: 103.37  E-value: 7.51e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  18 NVDTDQIIAKQFLKSIKRTGFGVNLFDDwryldegypgqdnstriINPDFIlnkPRYQGASILLARRNFGCGSSREHAPW 97
Cdd:PRK00439  10 NIDTDVIIPARYLNTSDPQELAKHCMED-----------------LDPEFA---KKVKPGDIIVAGKNFGCGSSREHAPI 69

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 521257151  98 ALSEYGFRTVIAPSFADIFYNNCFKNGmLPIVLDEEIVDTLmkatfaNEGYELTADLERQVVITPT-GEEYAFE-VDDF 174
Cdd:PRK00439  70 ALKAAGVSAVIAKSFARIFYRNAINIG-LPVLECDEAVDKI------EDGDEVEVDLETGVITNLTtGEEYKFKpIPEF 141
LEUD_arch TIGR02087
3-isopropylmalate dehydratase, small subunit; This subfamily is most closely related to the ...
 18-188 2.90e-24

3-isopropylmalate dehydratase, small subunit; This subfamily is most closely related to the 3-isopropylmalate dehydratase, small subunits which form TIGR00171. This subfamily includes the members of TIGR02084 which are gene clustered with other genes of leucine biosynthesis. The rest of the subfamily includes mainly archaeal species which exhibit two hits to this model. In these cases it is possible that one or the other of the hits does not have a 3-isopropylmalate dehydratase activity but rather one of the other related aconitase-like activities.


Pssm-ID: 273961 [Multi-domain]  Cd Length: 154  Bit Score: 93.64  E-value: 2.90e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   18 NVDTDQIIAKQFLKSIKRTGFGvnlfddwRYLDEGypgqdnstriINPDFILN-KPryqgASILLARRNFGCGSSREHAP 96
Cdd:TIGR02087   9 DIDTDEIIPGRYLRTTDPDELA-------SHAMEG----------IDPEFAKKvRP----GDVIVAGKNFGCGSSREQAA 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   97 WALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEIVdtlmkatfaNEGYELTADLERQVVITPTGEEYAFE-VDDFr 175
Cdd:TIGR02087  68 LALKAAGIAAVIAESFARIFYRNAINIGLPLIEAKTEGI---------KDGDEVTVDLETGEIRVNGNEEYKGEpLPDF- 137

                         170
                  ....*....|...
gi 521257151  176 khcLLNGLDDIGL 188
Cdd:TIGR02087 138 ---LLEILREGGL 147
leud TIGR02084
3-isopropylmalate dehydratase, small subunit; Homoaconitase, aconitase, and 3-isopropylmalate ...
 18-167 2.09e-21

3-isopropylmalate dehydratase, small subunit; Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. The members of the seed for this model are those sequences which are gene clustered with other genes involved in leucine biosynthesis and include some archaea. [Amino acid biosynthesis, Pyruvate family]


Pssm-ID: 131139 [Multi-domain]  Cd Length: 156  Bit Score: 86.38  E-value: 2.09e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151   18 NVDTDQIIAKQFLKSIKRTGFGVNLFDDwryldegypgqdnstriINPDFilnKPRYQGASILLARRNFGCGSSREHAPW 97
Cdd:TIGR02084   9 NVDTDVIIPARYLNTSDPKELAKHCMED-----------------LDKDF---VKKVKEGDIIVAGENFGCGSSREHAPI 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 521257151   98 ALSEYGFRTVIAPSFADIFYNNCFKNGmLPIVLDEEIVDTLmkatfaNEGYELTADLERQVVITPT-GEEY 167
Cdd:TIGR02084  69 AIKASGISCVIAKSFARIFYRNAINIG-LPIVESEEAVDEI------EEGDEVEVDLEKGIIKNLTkGKEY 132
HacB2_Meth NF040625
homoaconitase small subunit;
16-188 2.84e-21

homoaconitase small subunit;


Pssm-ID: 468597 [Multi-domain]  Cd Length: 161  Bit Score: 86.30  E-value: 2.84e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  16 RANVDTDQIIAKQFLKSIkrtgfgvNLFDDWRYLDEGypgqdnstriINPDFILNkprYQGASILLARRNFGCGSSREHA 95
Cdd:NF040625  12 GDNIDTDVIIPGRYLRTF-------NPDDLASHVMEG----------ERPDFTKN---VQKGDIIVAGWNFGCGSSREQA 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  96 PWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEEivdtlmkatfANEGYELTADLERQVVIT-PTGEEYAFE-VDD 173
Cdd:NF040625  72 PVAIKHAGVSAIIAKSFARIFYRNAINIGLPVIVADIE----------ADDGDILSIDLEKGIIKNkTTGEEFKIQpFKE 141

                        170
                 ....*....|....*
gi 521257151 174 FrkhcLLNGLDDIGL 188
Cdd:NF040625 142 F----MLEILEDGGL 152
PLN00072 PLN00072
3-isopropylmalate isomerase/dehydratase small subunit; Provisional
 12-168 1.11e-19

3-isopropylmalate isomerase/dehydratase small subunit; Provisional


Pssm-ID: 177701 [Multi-domain]  Cd Length: 246  Bit Score: 84.14  E-value: 1.11e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  12 CPLDRANVDTDQIIAKQFLKSIKRTGfgvnlfDDWRYLDE----GYPGQDNsTRIINPDfiLNKPRYqgaSILLARRNFG 87
Cdd:PLN00072  73 CFVVGDNIDTDQIIPAEYLTLVPSKP------DEYEKLGSyaliGLPAFYK-TRFVEPG--EMKTKY---SIIIGGENFG 140

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  88 CGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNG-MLPIVLDEEIVDTLmkatfaNEGYELTADLERQVVIT-PTGE 165
Cdd:PLN00072 141 CGSSREHAPVALGAAGAKAVVAESYARIFFRNSVATGeVYPLESEVRICEEC------KTGDVVTVELGNSVLINhTTGK 214


                 ...
gi 521257151 166 EYA 168
Cdd:PLN00072 215 EYK 217
PRK14023 PRK14023
homoaconitate hydratase small subunit; Provisional
 63-160 7.49e-18

homoaconitate hydratase small subunit; Provisional


Pssm-ID: 184460 [Multi-domain]  Cd Length: 166  Bit Score: 77.15  E-value: 7.49e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  63 INPDFilnKPRYQGASILLARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVlDEEIVDTLmkat 142
Cdd:PRK14023  39 LRPEF---ASTVRPGDILVAGRNFGLGSSREYAPEALKMLGIGAIIAKSYARIFYRNLVNLGIPPFE-SEEVVDAL---- 110

                         90
                 ....*....|....*...
gi 521257151 143 faNEGYELTADLERQVVI 160
Cdd:PRK14023 111 --EDGDEVELDLETGVLT 126
Aconitase_swivel cd00404
Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible ...
 63-153 5.46e-14

Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The aconitase family contains the following proteins: - Iron-responsive element binding protein (IRE-BP). IRE-BP is a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid.


Pssm-ID: 238236 [Multi-domain]  Cd Length: 88  Bit Score: 64.80  E-value: 5.46e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  63 INPDFILNKPRYqgasILLARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVldeeiVDTLMKAT 142
Cdd:cd00404    6 ITTDHISPAGPG----VVIGDENYGTGSSREHAALELRLLGGRAVIAKSFARIFFRNLVDQGLLPLE-----FADPEDYL 76

                         90
                 ....*....|.
gi 521257151 143 FANEGYELTAD 153
Cdd:cd00404   77 KLHTGDELDIY 87
AcnA_Bact_Swivel cd01579
Bacterial Aconitase-like swivel domain. Aconitase (aconitate hydratase or citrate hydrolyase) ...
 61-133 5.42e-11

Bacterial Aconitase-like swivel domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the course of the reaction. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. This distinct subfamily is found only in bacteria and archea. Its exact characteristics are not known.


Pssm-ID: 238811 [Multi-domain]  Cd Length: 121  Bit Score: 57.83  E-value: 5.42e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 521257151  61 RIINPDFIlNKPRYQGASILLARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPIVLDEE 133
Cdd:cd01579   34 HRVDPTFA-ERAKAAGPGFIVGGENYGQGSSREHAALAPMYLGVRAVLAKSFARIHRANLINFGILPLTFADE 105
PRK07229 PRK07229
aconitate hydratase; Validated
 75-156 8.57e-10

aconitate hydratase; Validated


Pssm-ID: 235974 [Multi-domain]  Cd Length: 646  Bit Score: 57.85  E-value: 8.57e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  75 QGASILLARRNFGCGSSREHApwALS-EY-GFRTVIAPSFADIFYNNCFKNGMLPIvldeeivdtlmkaTFANEgyeltA 152
Cdd:PRK07229 522 QGGGIVVGGENYGQGSSREHA--ALApRYlGVKAVLAKSFARIHKANLINFGILPL-------------TFADP-----A 581


                 ....
gi 521257151 153 DLER 156
Cdd:PRK07229 582 DYDK 585
Homoaconitase_Swivel cd01674
Homoaconitase swivel domain. This family includes homoaconitase and other uncharacterized ...
 53-158 1.26e-08

Homoaconitase swivel domain. This family includes homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase is part of an unusual lysine biosynthesis pathway found only in filamentous fungi, in which lysine is synthesized via the alpha-aminoadipate pathway. In this pathway, homoaconitase catalyzes the conversion of cis-homoaconitic acid into homoisocitric acid. The reaction mechanism is believed to be similar to that of other aconitases. This is the swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.


Pssm-ID: 238837 [Multi-domain]  Cd Length: 129  Bit Score: 51.52  E-value: 1.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521257151  53 YPG----QDNSTR-------IINPDFILNKPRYQGaSILLARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCF 121
Cdd:cd01674   12 YPGkytyQDDITPekmaevcMENYDSEFSTKTKQG-DILVSGFNFGTGSSREQAATALLAKGIPLVVSGSFGNIFSRNSI 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 521257151 122 KNGMLPIVLDEEIvdTLMKATFANEGYELT----ADLERQV 158
Cdd:cd01674   91 NNALLSIELPFLV--QKLREAFANESKELTrrtgWKLKWDV 129
AcnA_Mitochon_Swivel cd01578
Mitochondrial aconitase A swivel domain. Aconitase (also known as aconitate hydratase and ...
 78-128 5.87e-07

Mitochondrial aconitase A swivel domain. Aconitase (also known as aconitate hydratase and citrate hydro-lyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. In eukaryotes two isozymes of aconitase are known to exist: one found in the mitochondrial matrix and the other found in the cytoplasm. This is the mitochondrial form. The mitochondrial product is coded by a nuclear gene. Most members of this subfamily are mitochondrial but there are some bacterial members.


Pssm-ID: 238810 [Multi-domain]  Cd Length: 149  Bit Score: 47.46  E-value: 5.87e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 521257151  78 SILLARRNFGCGSSREHAPWALSEYGFRTVIAPSFADIFYNNCFKNGMLPI 128
Cdd:cd01578   71 WVVIGDENYGEGSSREHAALEPRHLGGRAIITKSFARIHETNLKKQGLLPL 121
AcnA COG1048
Aconitase A [Energy production and conversion]; Aconitase A is part of the Pathway/BioSystem: ...
 73-138 4.29e-04

Aconitase A [Energy production and conversion]; Aconitase A is part of the Pathway/BioSystem: Lysine biosynthesisTCA cycle


Pssm-ID: 440669 [Multi-domain]  Cd Length: 891  Bit Score: 40.86  E-value: 4.29e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 521257151  73 RYQGA---SILLARRNFGCGSSREHA---PWALseyGFRTVIAPSFADIFYNNCFKNGMLPIV-LDEEIVDTL 138
Cdd:COG1048  754 RYKAEgtpLVVLAGKEYGTGSSRDWAakgTRLL---GVKAVIAESFERIHRSNLVGMGVLPLQfPEGESAESL 823
AcnA_IRP_Swivel cd01580
Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, ...
 79-138 1.14e-03

Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals and may have the same role in other eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.


Pssm-ID: 238812 [Multi-domain]  Cd Length: 171  Bit Score: 38.41  E-value: 1.14e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 521257151  79 ILLARRNFGCGSSREHA---PWALseyGFRTVIAPSFADIFYNNCFKNGMLPI-VLDEEIVDTL 138
Cdd:cd01580   99 VILAGKEYGSGSSRDWAakgPFLL---GVKAVIAESFERIHRSNLVGMGILPLqFPPGENADSL 159
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH