1O8C,1TT7


Conserved Protein Domain Family
MDR_yhdh_yhfp

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cd05280: MDR_yhdh_yhfp 
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Yhdh and yhfp-like putative quinone oxidoreductases
Yhdh and yhfp-like putative quinone oxidoreductases (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction.
Statistics
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PSSM-Id: 176183
View PSSM: cd05280
Aligned: 38 rows
Threshold Bit Score: 335.28
Threshold Setting Gi: 225872125
Created: 26-Jul-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
NADP bindingdimer interface
Conserved site includes 27 residues -Click on image for an interactive view with Cn3D
Feature 1:NADP binding site [chemical binding site]
Evidence:
  • Structure:1O8C_D: Escherichia coli Yhdh binds NADP, contacts at 4A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                               ##                       
1O8C_D        22 LQALLLEQQDgk----------------tLASVQtldesrLPEGDVTVDVHWSSLNYKDALAITgkgkIIRNFPMIPGID 85  Escherichia coli
NP_891281     15 FDAFQVRRDTh-----------------iSAGLArlklddLSPGDLVIRTAYAGINYKDALATTdygkVIRKFPRVIGSD 77  Bordetella bron...
YP_298079      4 FLAYRLHDDGpdg--------------rvAGRFTelrfdnLPPGDVLIRVAYSGINYKDALAAAgrnaIVRQYPRTGGID 69  Ralstonia eutro...
YP_997267      4 FQALRLHDGKpe----------------pARRIEtlqpgdLSPGNVLIEVAYSSINHKDALAAHgrngIIRQFPRIGGID 67  Verminephrobact...
YP_001002651   4 FQAWRVSEAGke----------------dQGGVVtlggddLPAGDVLIRVAYSSLNYKDALAVTgqgkILRRFPMTPGID 67  Halorhodospira ...
YP_001209286   1 MKAIQVQKQGa-----------------aLVDLTaa---pVEKGFVAVQTLYSAVNYQDMLALTgraeALQRLPLIAGSD 60  Dichelobacter n...
YP_001628865  10 FQALVTRRIDgn----------------vQSAIEtvtlpqLSAGEVVVRTRYAGINYKDCLSIRgkakIITDYPRIAGIE 73  Bordetella petr...
EDY86828       3 HKALRVYDNGg-----------------aTAVLEtvetpkLEAGDVLIDAHYSSINFKDALAVTgkgkIMRRFPTTAGID 65  gamma proteobac...
EED39516       7 FTAFRIENDDag----------------yRSGLAelsvddLNPGQVLIRAHWSSVNYKDALAGTgkgrILRRFPLVGGID 70  Stenotrophomona...
YP_003145920   3 FLACRVFEKTesektesektspkvqkttiYHQLVqmetdeLTAGDVLIRVDYSSINYKDALAASgrgkIMKQFPLNAGID 82  Kangiella koree...
Feature 1                                                                     ##  #              
1O8C_D        86 FAGTVrtsedpRFHAGQEVLLTGWGVGenhWGGLAEQARVKgDWLVAMPQgLDARKAMIIGTAGFTAMLCVMALEdagvr 165 Escherichia coli
NP_891281     78 ASGWVvasrdpAFREGDEVAILGGGFGvdhDGGFSQYLRVPaGWAIRLPAgMTLRDAAALGIAGYTAALAVHLLQeagcr 157 Bordetella bron...
YP_298079     70 LSGHVaasddpRFREGDAVVVHGFGIGvdhDGGHAQYARVRgDWVMRLPEgLSPLEASTIGVAGYTAALALHWMEhnams 149 Ralstonia eutro...
YP_997267     68 LTGCVaasddaRFTPGDEVIVHGFGIGvdhDGGHAQRARVPgDWVLPLPRgLTLLEAAILGAAGYTAGLALHWMEhnglt 147 Verminephrobact...
YP_001002651  68 AAGVVaasdsaDVVPGDRVLVTGCGLGevhDGGFAEYVRVPaDWVVPVPAeVTVREAMALGTAGFTAALALIRMEaagqt 147 Halorhodospira ...
YP_001209286  61 AVGVVlsd-qgLFRRGDKIFCTGAGLGamyDGGLAEQVHLPlSAVFALPRdWSSKSAMLLGSAGFAAAQAILQLQqsgil 139 Dichelobacter n...
YP_001628865  74 AVGRVaasaddAFAPGDEVLVHGFQTGiafDGGFSEWMQVPaRHLQKLPPgLSAREAAILGVPGFTAAMALARFEsygla 153 Bordetella petr...
EDY86828      66 VAGVVeasedeRFQPGDQVLVNGYGLGensDGGLAEMVVTRaDYLVPLPEaFSMQDAMALGTAGFTAGISAYRMLqndqd 145 gamma proteobac...
EED39516      71 VAGTVvastdpDWREGDAVLATGCGLSetrDGGYSQYVRLEsRAVIAQPAgLSPREAMVLGTAGFTAALALLRMQdnrqt 150 Stenotrophomona...
YP_003145920  83 LAGVIvesdndAYQAGDKVLVNGCGIGeqyDGGLAQYARVKsDWVIKIPEaYDTRQAMIIGTAGFTAALAIHRMQvndqk 162 Kangiella koree...
Feature 1                 # ####                  ###                  #                    ##   
1O8C_D       166 pqdgeIVVTGASGGVGSTAVALLhKLGYqVVAVSGRe-sTHEYLKSLGASRVLPRdef-aesRPLEKqvWAGAIDTVGDK 243 Escherichia coli
NP_891281    158 pahgeVLVNGATGAVSSMGIEMLsGLGHaVTAVSAKa-dQHDYLRAVGAGAILAPadladngKPLEParWAAALDALGGP 236 Bordetella bron...
YP_298079    150 peqgpVVVSGATGGVGSMAVDILsARGYmVHAMSGKs-aEHAYLRSLGAGEILSPevasqpgKALEKarWAGAIDTVGGP 228 Ralstonia eutro...
YP_997267    148 pergpVLVTGATGGVASIAIDMLaGRGYqVTAMTGNs-dAHAALKALGASEVIGRigspaspKPLEKarWAGAVDSVGGQ 226 Verminephrobact...
YP_001002651 148 palgdVVVTGASGGVGSIAVDLFsNAGYrVIAVSGKe-pAAAYLRGLGAAEVVAPdaiglseRPLDRarFGGVVDTVGGP 226 Halorhodospira ...
YP_001209286 140 peqgeLLITGASGAVGLWAVKIAaYLGYdVVAVTRNpalHESLLLHHGASRLLALeslyassKALAKeqFAGGIDCLGGR 219 Dichelobacter n...
YP_001628865 154 paegpVAVSGANGAVGMLAISILaRAGYhIAAITRRp-eQADTLRRLGAAEIVDVrtaldstRPLESarYAAAIDNVGGN 232 Bordetella petr...
EDY86828     146 pemgkILVTGATGGVGSVATLLLsRLGFeVVALTGKaeqAGDYLSSLGAVQVLDRhalemtdKPLASveYAGAVDSVGGD 225 gamma proteobac...
EED39516     151 pdlgpLAVTGASGGVGALALSIFsRAGYsVHAVSGKp-dQADFLRGIGASEVLPReal-adtGPLQSarFGGGLDNAGGP 228 Stenotrophomona...
YP_003145920 163 pemgpIVVTGASGGVGSIAVNLLsKLGYeVIALTSRk-sMHDYLFELGANKVVSEdklgmsdKPLGKalFGGAIDNIGGK 241 Kangiella koree...
Feature 1                         #####                    ####                                  
1O8C_D       244 VLAKVLAQMnYGGCVAACGLAGGftLPTTVMPFILRNVRLQGVDSVMTpperRAQAWQRLVADLPes--fYTQAAKEISL 321 Escherichia coli
NP_891281    237 HLDLIVRSLmPRGCVASYGNVTGntLTTSVLPFILRGVRLIGVNLSYYid-qETALWQRLAGELKpr--rALEQVRAIGL 313 Bordetella bron...
YP_298079    229 VLAWMMRTMqPNGVIASVGNAGGpqLDTTVLPLILRGVRLLGINANSPma-lREAVWAKLAADYRpr--rLATIGQVIDF 305 Ralstonia eutro...
YP_997267    227 TLAWLTRTMqPEGIISAFGNIGGaeLDLTVLPFILRGIRLIGIDANSPmp-lRRQVWDKIARDYRpt--rLERIGHCITL 303 Verminephrobact...
YP_001002651 227 LLAGLLPQVeEYGNVAAIGLAGGvkLETTVMPWILRGVSLLGISSANCprglRLEGWRRLGDDLRpr-dpEGYITREVAL 305 Halorhodospira ...
YP_001209286 220 ALAAMLSQIrQQGAVAAIGVVTApdFTASLLPFIVRGIALFGITTHCSla-rREQVWQWLARYFDad-fiATMPYQEIFL 297 Dichelobacter n...
YP_001628865 233 VLAWLLRSMkDEGLVASVGNAGGnhYEGSVLPFIMRRVHLFGIVANAGwp-eRQRLWQKLAAEWRpgfeaLEPHVHAITL 311 Bordetella petr...
EDY86828     226 TLSWLTRVTaPEGNLASCGLAGGvkINTTVMPFILRGVNLLGINSVTLpmavRLKVWDMLAEHIKad-dlAAITRQVIGL 304 gamma proteobac...
EED39516     229 MLASLLAQTvPYGSVVSAGLAASptLDMTVMPFILRGVSLLGVSSANApralREEVWARLGSEWKpq-hlDRICTAEVGL 307 Stenotrophomona...
YP_003145920 242 TLSNIIAHTqLWGNVASIGLAQSpnLEAKVFPFILRGVSLLGISSTNCpmplRTKLWHQFGKELPlp-dfEAIVSKEIAL 320 Kangiella koree...
Feature 1                  #    #        
1O8C_D       322 s-eAPNFAEAIInnQIQGRTLVKV 344 Escherichia coli
NP_891281    314 e-eVAAQLRRMLdgQTTGRTVVDL 336 Bordetella bronchiseptica RB50
YP_298079    306 d-aLPDAMDRMLsrATRGRLVVRI 328 Ralstonia eutropha JMP134
YP_997267    304 a-qLPEYLGRMLqgQLQGRTVIRM 326 Verminephrobacter eiseniae EF01-2
YP_001002651 306 e-qLRDAAEAVLarQVTGRTLVRV 328 Halorhodospira halophila SL1
YP_001209286 298 devLPLARRWQM--LRAGRVIVRC 319 Dichelobacter nodosus VCS1703A
YP_001628865 312 p-eLPAHADRQLqgATSGRTLVDF 334 Bordetella petrii DSM 12804
EDY86828     305 d-eVIQHVGELMdgTMLGRYVVDL 327 gamma proteobacterium HTCC5015
EED39516     308 d-gLPAVFARMLagGSLGRTVVRI 330 Stenotrophomonas sp. SKA14
YP_003145920 321 e-dVSPYFDELIdkKHHGRLIVNC 343 Kangiella koreensis DSM 16069

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