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Conserved domains on  [gi|446556205|ref|WP_000633551|]
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pirin family protein [Salmonella enterica]

Protein Classification

pirin family protein( domain architecture ID 11448280)

pirin family protein such as quercetin 2,3-dioxygenase, a copper-containing enzyme that catalyzes the insertion of molecular oxygen into polyphenolic flavonols

CATH:  2.60.120.10
Gene Ontology:  GO:0046872
PubMed:  14697267|19478949
SCOP:  4000967

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YhaK COG1741
Redox-sensitive bicupin YhaK, pirin superfamily [General function prediction only];
14-231 1.61e-50

Redox-sensitive bicupin YhaK, pirin superfamily [General function prediction only];


:

Pssm-ID: 441347 [Multi-domain]  Cd Length: 253  Bit Score: 164.95  E-value: 1.61e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  14 DYGWLQARytfsfgHYF-DPTLLGYASLRVLNQEVLAP---GASFQPRTYPKVDILNLILDGEAEYRDSDGNHVQAKAGE 89
Cdd:COG1741    5 LGGGLKVR------RYLpSRDRRGFGPFRVLDHDGPAPpgyGAGFPPHPHRGMETVTYVLEGELEHRDSLGNGGVIRPGD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  90 ALLLAAQPGISYSEHNLSKVKPLTRMQLWLDACPERENA-----LVQKIP---LSAAQQQLLASP-DGEQNSLQLRQQVW 160
Cdd:COG1741   79 VQWMTAGSGIVHSERNPSEGGPLHGLQLWVNLPPADKGLapryqHIPDIPeveLGGGRLRVIAGPlDGVDGPVKIHQDAL 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446556205 161 VHHITLEKGESLNFQL-HGPRAYLQSIHGTFHAvtpneEREALTCGDGAFIRDEPNITLVADTPLRALLVDL 231
Cdd:COG1741  159 LYDIRLDAGATLTLPLpPGREAYLYVIEGSVTV-----NGETLEAGDLAVLSDGDELTLTADEDARVLLLGG 225
 
Name Accession Description Interval E-value
YhaK COG1741
Redox-sensitive bicupin YhaK, pirin superfamily [General function prediction only];
14-231 1.61e-50

Redox-sensitive bicupin YhaK, pirin superfamily [General function prediction only];


Pssm-ID: 441347 [Multi-domain]  Cd Length: 253  Bit Score: 164.95  E-value: 1.61e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  14 DYGWLQARytfsfgHYF-DPTLLGYASLRVLNQEVLAP---GASFQPRTYPKVDILNLILDGEAEYRDSDGNHVQAKAGE 89
Cdd:COG1741    5 LGGGLKVR------RYLpSRDRRGFGPFRVLDHDGPAPpgyGAGFPPHPHRGMETVTYVLEGELEHRDSLGNGGVIRPGD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  90 ALLLAAQPGISYSEHNLSKVKPLTRMQLWLDACPERENA-----LVQKIP---LSAAQQQLLASP-DGEQNSLQLRQQVW 160
Cdd:COG1741   79 VQWMTAGSGIVHSERNPSEGGPLHGLQLWVNLPPADKGLapryqHIPDIPeveLGGGRLRVIAGPlDGVDGPVKIHQDAL 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446556205 161 VHHITLEKGESLNFQL-HGPRAYLQSIHGTFHAvtpneEREALTCGDGAFIRDEPNITLVADTPLRALLVDL 231
Cdd:COG1741  159 LYDIRLDAGATLTLPLpPGREAYLYVIEGSVTV-----NGETLEAGDLAVLSDGDELTLTADEDARVLLLGG 225
cupin_Yhhw_N cd02910
Escherichia coli YhhW and YhaK and related proteins, pirin-like bicupin, N-terminal cupin ...
 17-127 2.95e-50

Escherichia coli YhhW and YhaK and related proteins, pirin-like bicupin, N-terminal cupin domain; This family includes the N-terminal cupin domains of YhhW and YhaK, Escherichia coli pirin-like proteins with unknown function. YhhW is structurally similar not only to human pirin but also to quercitin 2,3-dioxygenase (quercitinase). Although the function of YhhW is not completely understood, YhhW and its human ortholog have quercitinase activity and are likely to play an important role in transcription and apoptosis. This N-terminal cupin domain of YhhW has a metal coordination site and is thought to have catalytic activity while the C-terminal cupin-like domain has diverged considerably and has closer alignment with C-terminal pirin. YhaK is found in low abundance in the cytosol of E. coli and is strongly up-regulated by nitroso-glutathione (GSNO). There are major structural differences at the N-terminus of YhaK compared with YhhW; YhaK lacks the canonical cupin metal-binding residues of pirins and may be involved in chloride binding and/or sensing of oxidative stress in enterobacteria. YhaK showed no quercetinase and peroxidase activity; however, reduced YhaK was very sensitive to reactive oxygen species (ROS). Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380375  Cd Length: 119  Bit Score: 159.64  E-value: 2.95e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  17 WLQARYTFSFGHYFDPTLLGYASLRVLNQEVLAPGASFQPRTYPKVDILNLILDGEAEYRDSDGNHVQAKAGEALLLAAQ 96
Cdd:cd02910    1 WLKSRHTFSFADYYDPKNMGFGALRVINDDIVAPGTGFGTHPHRDMEIITYVLEGELTHRDSMGNKGVLKRGDVQRMSAG 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446556205  97 PGISYSEHNLSKVKPLTRMQLWLDacPEREN 127
Cdd:cd02910   81 TGIRHSEYNLSDTEPLRFLQIWIL--PDQRG 109
Pirin pfam02678
Pirin; This family consists of Pirin proteins from both eukaryotes and prokaryotes. The ...
 4-119 2.03e-37

Pirin; This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localized within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homolog of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily.


Pssm-ID: 426921  Cd Length: 104  Bit Score: 126.60  E-value: 2.03e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205    4 TRTAKQCGQAdyGWLQARYTFSFGHYFDPTLLGYASlrvlnqevlapGASFQPRTYPKVDILNLILDGEAEYRDSDGNHV 83
Cdd:pfam02678   2 FRVRRALGGA--GWLQSVDPFSFLDYFGPAEFGPGY-----------GAGFPPHPHRGFETVTYLLEGEVEHRDSLGNHG 68

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 446556205   84 QAKAGEALLLAAQPGISYSEHNLSKVKPLTRMQLWL 119
Cdd:pfam02678  69 VIRPGDVQWMTAGSGIVHSEMNPSEEGPLHGFQLWV 104
 
Name Accession Description Interval E-value
YhaK COG1741
Redox-sensitive bicupin YhaK, pirin superfamily [General function prediction only];
14-231 1.61e-50

Redox-sensitive bicupin YhaK, pirin superfamily [General function prediction only];


Pssm-ID: 441347 [Multi-domain]  Cd Length: 253  Bit Score: 164.95  E-value: 1.61e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  14 DYGWLQARytfsfgHYF-DPTLLGYASLRVLNQEVLAP---GASFQPRTYPKVDILNLILDGEAEYRDSDGNHVQAKAGE 89
Cdd:COG1741    5 LGGGLKVR------RYLpSRDRRGFGPFRVLDHDGPAPpgyGAGFPPHPHRGMETVTYVLEGELEHRDSLGNGGVIRPGD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  90 ALLLAAQPGISYSEHNLSKVKPLTRMQLWLDACPERENA-----LVQKIP---LSAAQQQLLASP-DGEQNSLQLRQQVW 160
Cdd:COG1741   79 VQWMTAGSGIVHSERNPSEGGPLHGLQLWVNLPPADKGLapryqHIPDIPeveLGGGRLRVIAGPlDGVDGPVKIHQDAL 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446556205 161 VHHITLEKGESLNFQL-HGPRAYLQSIHGTFHAvtpneEREALTCGDGAFIRDEPNITLVADTPLRALLVDL 231
Cdd:COG1741  159 LYDIRLDAGATLTLPLpPGREAYLYVIEGSVTV-----NGETLEAGDLAVLSDGDELTLTADEDARVLLLGG 225
cupin_Yhhw_N cd02910
Escherichia coli YhhW and YhaK and related proteins, pirin-like bicupin, N-terminal cupin ...
 17-127 2.95e-50

Escherichia coli YhhW and YhaK and related proteins, pirin-like bicupin, N-terminal cupin domain; This family includes the N-terminal cupin domains of YhhW and YhaK, Escherichia coli pirin-like proteins with unknown function. YhhW is structurally similar not only to human pirin but also to quercitin 2,3-dioxygenase (quercitinase). Although the function of YhhW is not completely understood, YhhW and its human ortholog have quercitinase activity and are likely to play an important role in transcription and apoptosis. This N-terminal cupin domain of YhhW has a metal coordination site and is thought to have catalytic activity while the C-terminal cupin-like domain has diverged considerably and has closer alignment with C-terminal pirin. YhaK is found in low abundance in the cytosol of E. coli and is strongly up-regulated by nitroso-glutathione (GSNO). There are major structural differences at the N-terminus of YhaK compared with YhhW; YhaK lacks the canonical cupin metal-binding residues of pirins and may be involved in chloride binding and/or sensing of oxidative stress in enterobacteria. YhaK showed no quercetinase and peroxidase activity; however, reduced YhaK was very sensitive to reactive oxygen species (ROS). Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380375  Cd Length: 119  Bit Score: 159.64  E-value: 2.95e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  17 WLQARYTFSFGHYFDPTLLGYASLRVLNQEVLAPGASFQPRTYPKVDILNLILDGEAEYRDSDGNHVQAKAGEALLLAAQ 96
Cdd:cd02910    1 WLKSRHTFSFADYYDPKNMGFGALRVINDDIVAPGTGFGTHPHRDMEIITYVLEGELTHRDSMGNKGVLKRGDVQRMSAG 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446556205  97 PGISYSEHNLSKVKPLTRMQLWLDacPEREN 127
Cdd:cd02910   81 TGIRHSEYNLSDTEPLRFLQIWIL--PDQRG 109
cupin_pirin-like_N cd20287
pirin-like, N-terminal cupin domain; This family contains the N-terminal cupin domain of pirin ...
 40-120 2.58e-38

pirin-like, N-terminal cupin domain; This family contains the N-terminal cupin domain of pirin and pirin-like proteins, including Escherichia coli YhhW and YhaK. Pirin functions as both a transcriptional cofactor and an apoptosis-related protein in mammals and is involved in seed germination and seedling development in plants. Proteins in this family have two tandem cupin-like folds but the C-terminal cupin fold has diverged considerably and does not have a metal binding site. The exact functions of pirins are unknown but they have quercitinase activity in Escherichia coli and are thought to play important roles in transcription and apoptosis. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380421 [Multi-domain]  Cd Length: 81  Bit Score: 128.09  E-value: 2.58e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  40 LRVLNQEVLAPGASFQPRTYPKVDILNLILDGEAEYRDSDGNHVQAKAGEALLLAAQPGISYSEHNLSKVKPLTRMQLWL 119
Cdd:cd20287    1 LRVFNEFVGGRGGGFPDHPHRGFEILSYLLEGS*EHEDSCGNTGQ*NAGELQW*SAGRGILHSE*NCSEDEPLHGLQLWV 80


                 .
gi 446556205 120 D 120
Cdd:cd20287   81 N 81
Pirin pfam02678
Pirin; This family consists of Pirin proteins from both eukaryotes and prokaryotes. The ...
 4-119 2.03e-37

Pirin; This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localized within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homolog of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily.


Pssm-ID: 426921  Cd Length: 104  Bit Score: 126.60  E-value: 2.03e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205    4 TRTAKQCGQAdyGWLQARYTFSFGHYFDPTLLGYASlrvlnqevlapGASFQPRTYPKVDILNLILDGEAEYRDSDGNHV 83
Cdd:pfam02678   2 FRVRRALGGA--GWLQSVDPFSFLDYFGPAEFGPGY-----------GAGFPPHPHRGFETVTYLLEGEVEHRDSLGNHG 68

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 446556205   84 QAKAGEALLLAAQPGISYSEHNLSKVKPLTRMQLWL 119
Cdd:pfam02678  69 VIRPGDVQWMTAGSGIVHSEMNPSEEGPLHGFQLWV 104
Pirin_C_2 pfam17954
Quercetinase C-terminal cupin domain; Experiments on the YhhW protein show that is has ...
 142-231 2.64e-24

Quercetinase C-terminal cupin domain; Experiments on the YhhW protein show that is has quercetinase activity. This entry represents the C-terminal cupin domain from the two cupin domains that make up the protein. This domain is usually associated with pfam02678.


Pssm-ID: 465583  Cd Length: 86  Bit Score: 92.14  E-value: 2.64e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446556205  142 LLASPDGEQNSLQLRQQVWVHHITLEKGESLNFQLHGPR-AYLQSIHGTfhaVTPNEEReaLTCGDGAFIRDEPNITLVA 220
Cdd:pfam17954   1 LIASPDGRDGSLKIHQDARLYAGLLDAGESLEYTLKPGRgAYLQVARGS---VEVNGQE--LEAGDGAAISDEDSLTITA 75

                          90
                  ....*....|.
gi 446556205  221 DTPLRALLVDL 231
Cdd:pfam17954  76 LEDAEVLLFDL 86
cupin_Yhhw_C cd20311
Escherichia coli YhhW and YhaK and related proteins, pirin-like bicupin, C-terminal cupin ...
 159-232 1.45e-21

Escherichia coli YhhW and YhaK and related proteins, pirin-like bicupin, C-terminal cupin domain; This family includes the C-terminal domain of YhhW and YhaK, Escherichia coli pirin-like proteins with unknown function. YhhW is structurally similar not only to human pirin but also to quercitin 2,3-dioxygenase (quercitinase). Although the function of YhhW is not completely understood, YhhW and its human ortholog have quercitinase activity and are likely to play an important role in transcription and apoptosis. This C-terminal cupin-like domain has diverged considerably and has closer alignment with C-terminal pirin, while the N-terminal cupin domain of YhhW has a metal coordination site and is thought to have catalytic activity. YhaK is found in low abundance in the cytosol of E. coli and is strongly up-regulated by nitroso-glutathione (GSNO). There are major structural differences at the N-terminus of YhaK compared with YhhW; YhaK lacks the canonical cupin metal-binding residues of pirins and may be involved in chloride binding and/or sensing of oxidative stress in enterobacteria. YhaK showed no quercetinase and peroxidase activity; however, reduced YhaK was very sensitive to reactive oxygen species (ROS). Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380445  Cd Length: 70  Bit Score: 84.51  E-value: 1.45e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446556205 159 VWVHHITLEKGESLNFQLHGPR-AYLQSIHGTFHAvtpneEREALTCGDGAFIRDEPNITLVADTPLRALLVDLP 232
Cdd:cd20311    1 AWLYASVLDKGEASVHLLAGGRrAWLQVVRGTVTV-----NGVALKTGDGAAISDETALTLTADSDAEVLLFDLP 70
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 47-107 1.34e-04

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 39.39  E-value: 1.34e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446556205  47 VLAPGASFQPRTYPKVDILNLILDGEAEYRDSDGNHVQAKAGEALLLaaQPGISYSEHNLS 107
Cdd:cd02208    5 TLPPGTSSPPHWHPEQDEIFYVLSGEGELTLDDGETVELKAGDIVLI--PPGVPHSFVNTS 63
 
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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