1O8C,1O89


Conserved Protein Domain Family
MDR_yhdh

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cd08288: MDR_yhdh 
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Yhdh putative quinone oxidoreductases
Yhdh 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: 176248
View PSSM: cd08288
Aligned: 41 rows
Threshold Bit Score: 397.293
Threshold Setting Gi: 148271782
Created: 1-May-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
NADP bindingdimer interface
Conserved site includes 28 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---tLASVQtld---esRLPEGDVTVDVHWSSLNYKDALAITGk-gKIIRNFPMIPGIDFAGTVRTSE 94  Escherichia coli
YP_001859381   8 FKAMLLREKDrt--ttSANLEtlt---vdQLPEGDTLVQIDYSTLNFKDALAVTGn-gKIVKTWPMVPGVDFSGTVVETT 81  Burkholderia ph...
YP_574974      2 PRALMLHDESp-----RARLEtld---edRLPERAVRVAIDYSDLNYKDAMAVTGq-gKIVRDYPLVPGIDFAGTVTAST 72  Chromohalobacte...
YP_952729      7 INAMVAHQDAe----gGIELRhevv-desFLPEGDVDIHVEYSSVNYKDALAVTPk-gGVARSYPLIPGIDVAGTVTSSR 80  Mycobacterium v...
YP_702746     18 FTAWIARENEg-----AIGLSqetv-desFLPQGEVTIQVEYSSVNFKDALALTPk-gGVVREYPIVPGIDVAGTVVESQ 90  Rhodococcus sp....
YP_445496      2 FSALVLDDTEge---iQAQVRelqtddlpRAESEEVHLEVLYSSLNYKDGLAVTGsgqVIRGDYPIVPGIDLVGRVLNTD 78  Salinibacter ru...
YP_121829      3 FRAMVAHESDsgivltRQELDe------nFLGQGAVTIKVHFSSANYKDALAITPg-gGVVRKYPIIPGIDLTGEVVSSD 75  Nocardia farcin...
EDZ60963       5 FKALIINQEGen---fTREVKsid---ksFLKHGDVTIKVDYSDLNFKDGMILKNg-gRLVKEFPHIPGIDFAGTVIESE 77  Candidatus Pela...
YP_002885857   5 FQALVLDQHEer---lHAEVKevqadvlpKEEDGNVLVEVHYSALNYKDALGLTTs-gKIVNRYPFIPGCEFVGTVVESD 80  Exiguobacterium...
YP_003290694   1 MRALVLYNENgt---iQPRIEtlp---edRLPEGDLLLEVHYSSLNYKDALAVTGrgkIIRGEYPFVPGIDLVGTVLESE 74  Rhodothermus ma...
Feature 1                                                            ##  #                       
1O8C_D        95 DPRFHAGQEVLLTGWGVGEnHWGGLAEQARVKGDWLVAMPQgLDARKAMIIGTAGFTAMLCVMALEDAGvrp---qdGEI 171 Escherichia coli
YP_001859381  82 HPRLAIGQRVVLTGWSVGEkHWGGYSQYQRIRGDWLVPIPEgLDSRLAMMIGTAGFTAMLCVIALERSGvtp---tsGAV 158 Burkholderia ph...
YP_574974     73 DARFDADDRVILTGWGVGErYWGGFAEAMRVDADWLVPCPRpLSTREAMLFGTAGLTAMLSVMRLQEAGlsp---gdGPV 149 Chromohalobacte...
YP_952729     81 SPEFAVGDRVIAHGQDIGTgRHGGYAQTARYPADYLVKLST-LSTSAAAAIGTAGFTAAMSVNAVRAHGisp---sdGPV 156 Mycobacterium v...
YP_702746     91 SPEFSVGDTVVAHGYDIGTaRHGGYAQFARVPADWVVKLDG-MSTRTAAAIGTAGFTAAMSVEALLSRGvep---gnGPV 166 Rhodococcus sp....
YP_445496     79 HDAFEEGDRVIGTGWQLGEvAWGGYRQEARVAGRKLVPLPDgLSPAQAMIIGTAGFTAMLSVMALGEHDvsp---gaGEV 155 Salinibacter ru...
YP_121829     76 SAEFAPGDQVVAHGYDIGVaHHGGFAEYARVPAEWVVKLDG-LSTRDAAAIGTAGFTAALSVQALLDRGltp---ddGAI 151 Nocardia farcin...
EDZ60963      78 NSKFKEGDEVILTGFRVGEvFYGGYSQIAKVNADFLVKKPKeLTSRQAMTLGTAGFTSLMSAFAIQAREsillgekvNDV 157 Candidatus Pela...
YP_002885857  81 YLDIKVGDEVIATGFGIGErHFGGFSQYAQVPGKWLVKLPKgMSMRDAIAIGTPGLTAMLSIDALEHAGvr----pgEEV 156 Exiguobacterium...
YP_003290694  75 NPDIKPGQTVIVTGWGIGEtHWGGYATRARVRSEWVVPLPRrLTPLEAMAIGTAGFTAMLSVMALEEHGlip---dqGEV 151 Rhodothermus ma...
Feature 1           # ####                  ###                 #                      ##        
1O8C_D       172 VVTGASGGVGSTAVALLHKLGYqVVAVSGResTHEYLKSLGASRVLPRDEFa---eSRPLEKQVWAGAIDTVGDKVLAKV 248 Escherichia coli
YP_001859381 159 LVTGAGGGVGSVAVTILSALGYsVSALTGDvgKHEYVLSLGAKECVDGPVWkd--aPRPLEAQRWSAAIDTVGSNVLARV 236 Burkholderia ph...
YP_574974    150 AVSGASGGVGSWAVSILAHEGFeVHAITGKpdQGDWLTRLGAAQVLARDDFte--rGRPLASTHWAGAVDTVGGQVLANL 227 Chromohalobacte...
YP_952729    157 LVTGATGGVGSVSVDLLAGLGYeVVASTGKadAHDLLRDLGAAEVIDRVPGpd-ekVRPLGKAHWAAVVDCVGGATLAYA 235 Mycobacterium v...
YP_702746    167 LVTGASGGVGTVAVDLLSAAGFeVVASSGKpeKAELLTELGASRVIGRLPEpd-tkPRPLGKAQWAAAVDCVGGATLAHV 245 Rhodococcus sp....
YP_445496    156 VVTGASGGAGSIAVALLDALGHeVVASTGSetAHAYLRALGADRIVHRRTLge-gpDRPMESGRWAGAIDAVGGDTLATL 234 Salinibacter ru...
YP_121829    152 LVTGATGGVGSVAVDILSGLGFeVIASTGKtdAGDLLSEIGANEVIGRLPEdpdakLRPLSKARWAGAVDSVGGRSLAYI 231 Nocardia farcin...
EDZ60963     158 LVTGATGGVGSVAVMALTKLGYnVTAVTGKdsKADYLKSLGAKNVVNRSEFdk--dPRLIDKGLWDGVVDTVGGKILANT 235 Candidatus Pela...
YP_002885857 157 LVTGATGGVGSFAITLLRRLGYhVVASTGKt-DSPYLRSLGVETIIDRSELeg--pARPLAKQRFDAAIDSVGGNTLANI 233 Exiguobacterium...
YP_003290694 152 VVTGASGGVGSLAVAILAHLGYdVVASTGKtsAYGLLQALGAARVIDRQELgq-gpKRPLDSGLWAGAVDTVGGPTLAAL 230 Rhodothermus ma...
Feature 1                    #####                    ####                                       
1O8C_D       249 LAQMnYGGCVAACGLAGGftLPTTVMPFILRNVRLQGVDSVMTPpeRRAQAWQRLVADLPes-fYTQAAKEISLseAPNF 327 Escherichia coli
YP_001859381 237 LAEMnYGGTVAACGLAGGpdLPTTVMPFILRGVRLLGVDSVMLPyaERLATWQRVSRDLPkavlERIAARTVSLdeVRDA 316 Burkholderia ph...
YP_574974    228 LAQMrYAGKVAAVGLAGDaaLPTTVMPFILRGVALLGVDSVYIPfeRRRAAWQRIAALPNal-lTHMQVEEIGLedVESQ 306 Chromohalobacte...
YP_952729    236 LSTTkYGGVAAASGLAGSpdLPATVLPFILRGVTLAGIDSVLLPiaKRRDIWAQIESELLpr-hLARITRDVPVrqVADV 314 Mycobacterium v...
YP_702746    246 LSTIeYGGAVAASGLTGGpkLETTVLPFILRGVSLLGIDSVQYPidQRRRLWGRLASDLAps-rLESITHDVPIadVVSV 324 Rhodococcus sp....
YP_445496    235 IAQLkRHGSVASFGNAGGheLRTTVLPFILRGVNLLGIDSNTCPndRRRTAWGRLAQLLTeahfDRIHARTISLadIPEA 314 Salinibacter ru...
YP_121829    232 LSSIgYGGTVAASGLTGGpdLPATVMPFILRGVALIGIDSVAYPieKRRALWSRLTTDFRpr-hLTQLENHAPVtdAERV 310 Nocardia farcin...
EDZ60963     236 IVQTkPNGIIAVCGNANNneLNTSVIPFMLRGIKLWGMDSANCGikRREFIWSEASKLIDfe-lLEKSILTVSLdeLIDT 314 Candidatus Pela...
YP_002885857 234 LSQIrYEGAVAACGLVGGaeLPTSVYPFILRGVKLIGIDSVMQPmvRRTNAWERLEELIDlk-vLNEMIHEIPLhdVLRH 312 Exiguobacterium...
YP_003290694 231 LSQLkRHGSVAACGLAQSheFTTTVFPFILRGINLLGIDSNTCPqeRRRRAWHRLTHDLPkd-aLHRVTRVIPLseVPQW 309 Rhodothermus ma...
Feature 1           #  # #        
1O8C_D       328 AEAIInNQIQGRTLVKV 344 Escherichia coli
YP_001859381 317 ASDLLsGKLKGRVLVDV 333 Burkholderia phymatum STM815
YP_574974    307 AHAMIeGRTHGRLLIDP 323 Chromohalobacter salexigens DSM 3043
YP_952729    315 LGAIIgGGVTGRTRVVV 331 Mycobacterium vanbaalenii PYR-1
YP_702746    325 IDQVRaGTYSGRAVVGV 341 Rhodococcus sp. RHA1
YP_445496    315 SRALLaGEVQGRILVDV 331 Salinibacter ruber DSM 13855
YP_121829    311 LHAIKnGTHSRRTVLGV 327 Nocardia farcinica IFM 10152
EDZ60963     315 YPKILkGEISGRVIVDL 331 Candidatus Pelagibacter sp. HTCC7211
YP_002885857 313 AEAMMrGELSGRTIVRL 329 Exiguobacterium sp. AT1b
YP_003290694 310 SEAMLaGKTQGRLVVDV 326 Rhodothermus marinus DSM 4252

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