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Conserved domains on  [gi|61680713|pdb|1YLL|A]
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Chain A, Crystal Structure of the Conserved Protein of Unknown Function PA5104 from Pseudomonas aeruginosa PAO1

Protein Classification

HutD family protein( domain architecture ID 10007956)

HutD family protein similar to Pseudomonas fluorescens histidine utilization protein HutD

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ves COG3758
Various environmental stresses-induced protein Ves (function unknown) [Function unknown];
3-199 2.78e-67

Various environmental stresses-induced protein Ves (function unknown) [Function unknown];


:

Pssm-ID: 442972 [Multi-domain]  Cd Length: 196  Bit Score: 204.42  E-value: 2.78e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A        3 MSeLRILRAVDYPR*PWKNGAGSTEEIARDGGDGLDGF-GWRLSIADVGESGGFSGFAGYQRIISVLEGGG*RLRVDGAE 81
Cdd:COG3758   1 MS-MRILRAADLPRMPWKNGGGETREIARFPEGAGLDDfDWRLSIATVAQDGPFSAFPGIDRTITLLEGDGLRLTVDGQG 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A       82 SAPLRAR-QAFAFSGDSEVHCTLLDGAIRDFNLIYAPRRHRARLQWLRVEGELDWHGTASTLLLFAQQDGVAISLqGQPR 160
Cdd:COG3758  80 EHTLDEPfQPFAFSGDAPVSARLLGGPVRDFNLMTRRGRARARVRVLRLAGTLPLHADAGTGLLYVLAGAWTVAL-GGEA 158

                       170       180       190
                ....*....|....*....|....*....|....*....
1YLL_A      161 GQLAAHDCLCAEGLQGLQHWRLTAHEpAWVCAVELDSLG 199
Cdd:COG3758 159 ITLEAGDTLLLEAPAPLLTLTPLSGD-GRLLLVELTPRA 196
 
Name Accession Description Interval E-value
Ves COG3758
Various environmental stresses-induced protein Ves (function unknown) [Function unknown];
3-199 2.78e-67

Various environmental stresses-induced protein Ves (function unknown) [Function unknown];


Pssm-ID: 442972 [Multi-domain]  Cd Length: 196  Bit Score: 204.42  E-value: 2.78e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A        3 MSeLRILRAVDYPR*PWKNGAGSTEEIARDGGDGLDGF-GWRLSIADVGESGGFSGFAGYQRIISVLEGGG*RLRVDGAE 81
Cdd:COG3758   1 MS-MRILRAADLPRMPWKNGGGETREIARFPEGAGLDDfDWRLSIATVAQDGPFSAFPGIDRTITLLEGDGLRLTVDGQG 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A       82 SAPLRAR-QAFAFSGDSEVHCTLLDGAIRDFNLIYAPRRHRARLQWLRVEGELDWHGTASTLLLFAQQDGVAISLqGQPR 160
Cdd:COG3758  80 EHTLDEPfQPFAFSGDAPVSARLLGGPVRDFNLMTRRGRARARVRVLRLAGTLPLHADAGTGLLYVLAGAWTVAL-GGEA 158

                       170       180       190
                ....*....|....*....|....*....|....*....
1YLL_A      161 GQLAAHDCLCAEGLQGLQHWRLTAHEpAWVCAVELDSLG 199
Cdd:COG3758 159 ITLEAGDTLLLEAPAPLLTLTPLSGD-GRLLLVELTPRA 196
HutD pfam05962
HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and ...
 11-192 9.68e-60

HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and utilization operon. HutD is operonic with the well characterized repressor protein HutC. Genetic analysis using transcriptional fusions (lacZ) and deletion mutants shows that hutD is necessary to maintain fitness in environments replete with histidine. Evidence outlined by Zhang _ Rainey (2007) suggests that HutD functions as a governor that sets an upper bound on the level of hut operon transcription. The mechanistic basis is unknown, but in silico molecular docking studies based on the crystal structure of PA5104 (HutD from Pseudomonas aeruginosa) show that urocanate (the first breakdown product of histidine) docks with the active site of HutD.


Pssm-ID: 428694 [Multi-domain]  Cd Length: 180  Bit Score: 184.83  E-value: 9.68e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A         11 AVDYPR*PWKNGAGSTEEIARDGGDGLDGF-GWRLSIADVGESGGFSGFAGYQRIISVLEGGG*RLRVDGaESAPLRARQ 89
Cdd:pfam05962   1 AADYRRMPWKNGGGVTREIAIHPEGAGLDDfDWRLSIATVAQDGPFSAFPGIDRTLSLLEGDGMRLSVDG-PSRLLAPYQ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A         90 AFAFSGDSEVHCTLLDGAIRDFNLIYAPRRHRARLQWLRVEGELDWH-GTASTLLLFAQQDGVAISLQGQPRGQLAAHDC 168
Cdd:pfam05962  80 PFAFSGDAPVSARLLGGPIRDFNLMTRRGRATARVERLPLVGGLTLAaDGASTLLLYCLKGQVSVALDGGGTHTLAAGDC 159

                         170       180
                  ....*....|....*....|....
1YLL_A        169 LCAEGLQGLqhwRLTAHEPAWVCA 192
Cdd:pfam05962 160 LLLEGPAAL---RLTLDGKGALLL 180
cupin_HutD_N cd20293
histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model ...
 24-115 4.21e-42

histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model represents the N-terminal domain of a bicupin protein HutD, involved in histidine utilization (Hut) in Pseudomonas species. Although a metal binding site is not found in Pseudomonas fluorescens (PfluHutD), a binding pocket for ligands is located in the middle of the N-terminal cupin domain near the metal binding sites; N-formyl-l-glutamate (FG, a Hut pathway intermediate) has been identified as a potential ligand in vivo. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380427  Cd Length: 92  Bit Score: 136.83  E-value: 4.21e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A       24 GSTEEIARDGGDGLDGFGWRLSIADVGESGGFSGFAGYQRIISVLEGGG*RLRVDGAESAPLRARQAFAFSGDSEVHCTL 103
Cdd:cd20293   1 GTTREIARSPGGAGDDFDWRLSIADVAQDGPFSAFPGIDRILTVLEGAGMVLTVDGGEQVLLRPLQPFAFSGDAAVSARL 80

                        90
                ....*....|..
1YLL_A      104 LDGAIRDFNLIY 115
Cdd:cd20293  81 LDGPVRDFNLMT 92
PRK11396 PRK11396
environmental stress-induced protein Ves;
19-157 1.57e-15

environmental stress-induced protein Ves;


Pssm-ID: 236905 [Multi-domain]  Cd Length: 191  Bit Score: 71.42  E-value: 1.57e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A        19 WKNGAGSTEEIArDGGDGLDGFGWRLSIADVGESGGFSGFAGYQRIISVLEGGG*RLRVDGAESAPLRARQAFAFSGDSE 98
Cdd:PRK11396  14 WRNAAGETREIC-TFPPAKRDFYWRASIASIAANGEFSLFPGMERIVTLLEGGEMFLESADRFNHTLKPLQPFAFAADQV 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A        99 VHCTLLDGAIR-DFNLIyaPRRHRARLQwLRVegeldwhgTASTLLLFAQQDGVAISLQG 157
Cdd:PRK11396  93 VKAKLTAGQMSmDFNIM--TRLDVCKAK-VRI--------AERTFTTFGSRGGVVFVING 141
 
Name Accession Description Interval E-value
Ves COG3758
Various environmental stresses-induced protein Ves (function unknown) [Function unknown];
3-199 2.78e-67

Various environmental stresses-induced protein Ves (function unknown) [Function unknown];


Pssm-ID: 442972 [Multi-domain]  Cd Length: 196  Bit Score: 204.42  E-value: 2.78e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A        3 MSeLRILRAVDYPR*PWKNGAGSTEEIARDGGDGLDGF-GWRLSIADVGESGGFSGFAGYQRIISVLEGGG*RLRVDGAE 81
Cdd:COG3758   1 MS-MRILRAADLPRMPWKNGGGETREIARFPEGAGLDDfDWRLSIATVAQDGPFSAFPGIDRTITLLEGDGLRLTVDGQG 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A       82 SAPLRAR-QAFAFSGDSEVHCTLLDGAIRDFNLIYAPRRHRARLQWLRVEGELDWHGTASTLLLFAQQDGVAISLqGQPR 160
Cdd:COG3758  80 EHTLDEPfQPFAFSGDAPVSARLLGGPVRDFNLMTRRGRARARVRVLRLAGTLPLHADAGTGLLYVLAGAWTVAL-GGEA 158

                       170       180       190
                ....*....|....*....|....*....|....*....
1YLL_A      161 GQLAAHDCLCAEGLQGLQHWRLTAHEpAWVCAVELDSLG 199
Cdd:COG3758 159 ITLEAGDTLLLEAPAPLLTLTPLSGD-GRLLLVELTPRA 196
HutD pfam05962
HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and ...
 11-192 9.68e-60

HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and utilization operon. HutD is operonic with the well characterized repressor protein HutC. Genetic analysis using transcriptional fusions (lacZ) and deletion mutants shows that hutD is necessary to maintain fitness in environments replete with histidine. Evidence outlined by Zhang _ Rainey (2007) suggests that HutD functions as a governor that sets an upper bound on the level of hut operon transcription. The mechanistic basis is unknown, but in silico molecular docking studies based on the crystal structure of PA5104 (HutD from Pseudomonas aeruginosa) show that urocanate (the first breakdown product of histidine) docks with the active site of HutD.


Pssm-ID: 428694 [Multi-domain]  Cd Length: 180  Bit Score: 184.83  E-value: 9.68e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A         11 AVDYPR*PWKNGAGSTEEIARDGGDGLDGF-GWRLSIADVGESGGFSGFAGYQRIISVLEGGG*RLRVDGaESAPLRARQ 89
Cdd:pfam05962   1 AADYRRMPWKNGGGVTREIAIHPEGAGLDDfDWRLSIATVAQDGPFSAFPGIDRTLSLLEGDGMRLSVDG-PSRLLAPYQ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A         90 AFAFSGDSEVHCTLLDGAIRDFNLIYAPRRHRARLQWLRVEGELDWH-GTASTLLLFAQQDGVAISLQGQPRGQLAAHDC 168
Cdd:pfam05962  80 PFAFSGDAPVSARLLGGPIRDFNLMTRRGRATARVERLPLVGGLTLAaDGASTLLLYCLKGQVSVALDGGGTHTLAAGDC 159

                         170       180
                  ....*....|....*....|....
1YLL_A        169 LCAEGLQGLqhwRLTAHEPAWVCA 192
Cdd:pfam05962 160 LLLEGPAAL---RLTLDGKGALLL 180
cupin_HutD_N cd20293
histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model ...
 24-115 4.21e-42

histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model represents the N-terminal domain of a bicupin protein HutD, involved in histidine utilization (Hut) in Pseudomonas species. Although a metal binding site is not found in Pseudomonas fluorescens (PfluHutD), a binding pocket for ligands is located in the middle of the N-terminal cupin domain near the metal binding sites; N-formyl-l-glutamate (FG, a Hut pathway intermediate) has been identified as a potential ligand in vivo. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380427  Cd Length: 92  Bit Score: 136.83  E-value: 4.21e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A       24 GSTEEIARDGGDGLDGFGWRLSIADVGESGGFSGFAGYQRIISVLEGGG*RLRVDGAESAPLRARQAFAFSGDSEVHCTL 103
Cdd:cd20293   1 GTTREIARSPGGAGDDFDWRLSIADVAQDGPFSAFPGIDRILTVLEGAGMVLTVDGGEQVLLRPLQPFAFSGDAAVSARL 80

                        90
                ....*....|..
1YLL_A      104 LDGAIRDFNLIY 115
Cdd:cd20293  81 LDGPVRDFNLMT 92
cupin_HutD_C cd20490
histidine utilization protein HutD and related proteins, C-terminal cupin domain; This model ...
 120-195 2.14e-32

histidine utilization protein HutD and related proteins, C-terminal cupin domain; This model represents the C-terminal domain of a bicupin protein HutD, involved in histidine utilization (Hut) in Pseudomonas species. Although a metal binding site is not found in Pseudomonas fluorescens (PfluHutD), a binding pocket for ligands is located in the middle of the N-terminal cupin domain near the metal binding sites; N-formyl-l-glutamate (FG, a Hut pathway intermediate) has been identified as a potential ligand in vivo. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380447  Cd Length: 77  Bit Score: 111.55  E-value: 2.14e-32
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
1YLL_A      120 HRARLQWLRVEGELDWHGTASTLLLFAQQDGVAISLQGQPRGQLAAHDCLCAEGLQGLQHWRLTAHEPAWVCAVEL 195
Cdd:cd20490   1 YRARLQWLAGEGEQRFFSSASTVLLFSAGEGLAVSLDGHAAQQLGRHDCLQLEGNAGLAELRLSGAGAGRCCLIEL 76
PRK11396 PRK11396
environmental stress-induced protein Ves;
19-157 1.57e-15

environmental stress-induced protein Ves;


Pssm-ID: 236905 [Multi-domain]  Cd Length: 191  Bit Score: 71.42  E-value: 1.57e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A        19 WKNGAGSTEEIArDGGDGLDGFGWRLSIADVGESGGFSGFAGYQRIISVLEGGG*RLRVDGAESAPLRARQAFAFSGDSE 98
Cdd:PRK11396  14 WRNAAGETREIC-TFPPAKRDFYWRASIASIAANGEFSLFPGMERIVTLLEGGEMFLESADRFNHTLKPLQPFAFAADQV 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
1YLL_A        99 VHCTLLDGAIR-DFNLIyaPRRHRARLQwLRVegeldwhgTASTLLLFAQQDGVAISLQG 157
Cdd:PRK11396  93 VKAKLTAGQMSmDFNIM--TRLDVCKAK-VRI--------AERTFTTFGSRGGVVFVING 141
 
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.
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