2H6E,1H2B,1R37


Conserved Protein Domain Family
arabinose_DH_like

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cd05284: arabinose_DH_like 
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D-arabinose dehydrogenase
This group contains arabinose dehydrogenase (AraDH) and related alcohol dehydrogenases. AraDH is a member of the medium chain dehydrogenase/reductase family and catalyzes the NAD(P)-dependent oxidation of D-arabinose and other pentoses, the initial step in the metabolism of d-arabinose into 2-oxoglutarate. Like the alcohol dehydrogenases, AraDH binds a zinc in the catalytic cleft as well as a distal structural zinc. AraDH forms homotetramers as a dimer of dimers. AraDH replaces a conserved catalytic His with replace with Arg, compared to the canonical ADH site. 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: 176187
View PSSM: cd05284
Aligned: 33 rows
Threshold Bit Score: 351.478
Threshold Setting Gi: 54024234
Created: 27-Jul-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 23 residues -Click on image for an interactive view with Cn3D
Feature 1:NAD binding site [chemical binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                  ###  #                                
2H6E_A         4 SKAALLKKFs----EPLSIEDVNIPEPq-gEEVLIRIGGAGVCRTDLRVWKGveak------qgfrLPIILGHENAGTIV 72  Sulfolobus solf...
1R37_A         1 MRAVRLVEIg----KPLSLQEIGVPKPk-gPQVLIKVEAAGVCHSDVHMRQGrfgnlrivedlgvkLPVTLGHEIAGKIE 75  Sulfolobus solf...
NP_375899      1 MKAMLIKEFg----KPLKLEDVDVPKLk-qNQVLIRVRSAGVCHTDVSVRSGtiykrv--svnppkLPFIPGHEIAGIIE 73  Sulfolobus toko...
NP_559727      8 HKAAFFYEIa----GPFKIDEVPTPEEvppYGLLVKTRSVGICHSDLHLWQGdyksi----glpksLPWIVGHEIVGTIA 79  Pyrobaculum aer...
Q4J781         1 MKAMLLHKFg----EPLRLEDMDVPKVg-vGQVLVKVDYAGVCHTDLSVRSGaifnri--ssskptLPLVIGHEIAGEVV 73  Sulfolobus acid...
YP_708167      1 MIAAVIPEF-----GRMKVREVDDPQLsgsTDVIVKVAAAGVCRTDLETMSGglvpa----ygqpiFPYVAGHETTGWVE 71  Rhodococcus sp....
YP_765916      1 MKAARILEYk----KALVLEDIPVPDIq-pDEVLVKVAACGMCRSDVLLIDGffqgy-----gdipPPVIPGHEITGTIE 70  Rhizobium legum...
YP_001540737   5 MRAMRLVEFg----KPLKLQEVPIPKPk-gTEVLIKVEGAGVCHSVVHFVDGrfgridv-kalglrIPVTPGHEIAGTVA 78  Caldivirga maqu...
YP_001540992   3 ARALVLREFs----GRLRLESIDVKEPgndESVLVKVIGAGMCKTDVRLWKGtepr------egfkLPFVLGHENAGIVE 72  Caldivirga maqu...
YP_002565402   1 MQAARLHEYtddmsEGLAIDEVDRPHAtgpSDVIVEVEGAGWCQTDNHIIEGmweey-----vpqtLPMTLGHENAGTVV 75  Halorubrum lacu...
Feature 1                                                                                        
2H6E_A        73 EVGELA----KVKKGDNVVVYATW-GDLTCRYCREGkFNICKNQIIPGQ--TTNGGFSEYMLVksSRWLVKLNSl--sPV 143 Sulfolobus solf...
1R37_A        76 EVGDEVv---GYSKGDLVAVNPWQ-GEGNCYYCRIGeEHLCDSPRWLGI--NFDGAYAEYVIVphYKYMYKLRRl--nAV 147 Sulfolobus solf...
NP_375899     74 DVGDEVi---GFTKGDKVIVNPWQ-GEGNCYYCKIGeEQYCDFPTWLGI--STNGGYAEYVVSn-FNYVYKVNKl--sVE 144 Sulfolobus toko...
NP_559727     80 KKGSLVp--eSLREGTPVLVYAWQpADENDEIVAEGyTQLASRRRRYAF--DIEGGLQEYIVVp-HYKYVIPLEgfeeIE 154 Pyrobaculum aer...
Q4J781        74 ELGGNVe---GFKKSDKVLIDPWI-GDGSCHYCKIGeDQYCDNPKWLGI--NVNGGYGEYVLVp-DYRYMFKLRnl-sTS 145 Sulfolobus acid...
YP_708167     72 AVGSEVs---VVAPGDPVLLHPLI-TCGLCDGCRAGrDMYCSNSRFPGVdaTTWGGFAEYMLTg-ERAVVPLPGda-dLV 145 Rhodococcus sp....
YP_765916     71 KIGSVVpkvaGIEEGDHVVVAPGW-GDGVCRHCMVGdTHICPNVRWPGF--GPDGGFAEYIPVp-ARYVIKVPKhl-kFE 145 Rhizobium legum...
YP_001540737  79 AVGDDVe---GVKEGDRVAVDPWI-GDGTCHYCKLGeEQLCEHPIKIGE--NIDGGFAEYVLIp-HYRYLYVLRnl-dTV 150 Caldivirga maqu...
YP_001540992  73 EVGGKVk---GLKPGDKVLVYAIW-ADPGCKYCRVGkCMQCRDQSIPGQs-NYYGGYAEYLYVp-DYRYLVRIDi--dPV 144 Caldivirga maqu...
YP_002565402  76 ETGDDVd---IVSEGDPVICHPVQ-TCGTCRPCRLGeTMYCENSAFNGL--TTDGGFAEYLHTs-ERSVIPLPSgv-dPI 147 Halorubrum lacu...
Feature 1              #   #                       # ## #                    ##                  
2H6E_A       144 EAAPLADAGTTSMGAIRQALPFISkfaePVVIVNGIGG-LAVYTIQILKALMknITIVGISRSKKHRDFALELGADYVSE 222 Sulfolobus solf...
1R37_A       148 EAAPLTCSGITTYRAVRKASLDPT----KTLLVVGAGGgLGTMAVQIAKAVSg-ATIIGVDVREEAVEAAKRAGADYVIN 222 Sulfolobus solf...
NP_375899    145 EASPLACAGVTAYRAARLANLTPS----KYVMVIGAGGgLGSFGVQIVKALYg-STVIAVDINEEGLKLASRLGSDYVMN 219 Sulfolobus toko...
NP_559727    155 SIAPLGCAGLTTYNAVKKIRKYIRp--dDYILIVGLGG-LGIYAVQWAKVLLpeANIIAVDIREEALQFASKIVRDVVYT 231 Pyrobaculum aer...
Q4J781       146 TASPLACSGVTAYRALRLANLDPS----KSVMIIGAGGgLGSIAVQIAKAIHg-SFIIGVDVSEEGLKLATNLGADYVTS 220 Sulfolobus acid...
YP_708167    146 ELAGFSDAGLTAYHAVKRLVPYLNp--nGTVAVIGVGG-VGHFAVQLLREMTs-CTVIALDVDSARAQLGEQLGAHASFH 221 Rhodococcus sp....
YP_765916    146 QLAPLTDAGLTPYRGLKKIRNAGGlgpdRVIGVFGIGG-LGAYAVQYAKLLGagGPVVAVARNEEKLQVAKKYGADHIIA 224 Rhizobium legum...
YP_001540737 151 NASPLPCAGLTPYRALVRKAQVKPs---EYVAVIGAGGgLGTMAIQIAKVMG--AIVIGIDVRDEALKEIERAGADYVIN 225 Caldivirga maqu...
YP_001540992 145 ETAPLADAGLTSYSAVKKSIPYLYp--gSLVIVYGMGG-LASYAVQYLRKMTpyVTVVAVSRSDDKLKWAEELGAHYAVH 221 Caldivirga maqu...
YP_002565402 148 DIAPHADAGITAYHAVKKAVADLNp--gDHAVVIGVGG-LGHIGLQCLDAMSa-ARITAVDLKESALDLAEGYGADHLIN 223 Halorubrum lacu...
Feature 1                                   ##    #                ###                        ###
2H6E_A       223 MKda-----eSLINKLTDglGASIAIDLVGTeETTYNLGKLLaqEGAIILVGMEGkrVSLEAFdta---vwNKKLLGSNY 294 Sulfolobus solf...
1R37_A       223 ASmqd---plAEIRRITEskGVDAVIDLNNSeKTLSVYPKALakQGKYVMVGLFGadLHYHAPlit---lsEIQFVGSLV 296 Sulfolobus solf...
NP_375899    220 AKdqs---llQEILRITEgrGVDAILDFVGSeSTTKNYYTILakLGRYIKVGTFG--GGLPQEaglklhsmGWEFIGTLT 294 Sulfolobus toko...
NP_559727    232 KVnan---tiEILNEITKgrGVRAVIDLVSNnNTVPIYSKILttKGVYNLVGLMGheVTIPTQili---rkEIVIITTYT 305 Pyrobaculum aer...
Q4J781       221 KVde-----eEVRKITTGr-GVDAIIDFVGSeFTTSNYYTLLakLGRYVKVGTYG--GGLPHDaglrlhsmGWQFIGTLT 292 Sulfolobus acid...
YP_708167    222 GPiet---llESVLELTNg-GVDAVMDCASGgSQSVTPLDFVrkGGTVSLVGGGAs-LNVDTLsav---vkEITIVTNLV 293 Rhodococcus sp....
YP_765916    225 IEgkssedvgKELRKATGqdKFDAIIDCAGAtEMMQLAFSRLaiSGHYADVGFIGdrIDIPLFprv---sgEQTFHGSFW 301 Rhizobium legum...
YP_001540737 226 GRgn----vvEEVRKITGgrGVNVIVDTVGSnETLGTYIDALdkLGRYIILGLYGgdLTYHAPyit---qrEIQIMGSLT 298 Caldivirga maqu...
YP_001540992 222 PSe------lASIVKSVStdGASILLDFVGN-EESAKAVSLLepGGAVVLVGMEGksYPIPVFdtv---awQYTVIGSNY 291 Caldivirga maqu...
YP_002565402 224 PSddd---vrEELAGITDgtGAAQVLDFVGAdITTAYAPDITaaGGDHHIIGYGGh-VHEPAQalv---ngEFSFVGNIV 296 Halorubrum lacu...
Feature 1                                               #       #     
2H6E_A       295 GSlNDLEDVVRLSesGKIKPYIIKVpl---dDINKAFTNLDEGRVDGRQVITP 344 Sulfolobus solfataricus
1R37_A       297 GNqSDFLGIMRLAeaGKVKPMITKTmk--leEANEAIDNLENFKAIGRQVLIP 347 Sulfolobus solfataricus
NP_375899    295 GNrRDFLEIIKLAesGKIRIVITKLsl---eEANEALNNLESNKVTGRQVLIP 344 Sulfolobus tokodaii str. 7
NP_559727    306 GSlADQINVIKLAkkINYKEVISERfkfteeDVNKAFNKLKEGKILGRGIIVF 358 Pyrobaculum aerophilum str. IM2
Q4J781       293 GNrKDFLEVLELAenGKIKPMITKVls--leEANDALDNLEKGKVSGRQVLKV 343 Sulfolobus acidocaldarius
YP_708167    294 GTyTELQELIGMQrsGLRSLHTTFPl----sDTTEALHALTTGSVAGRAVLVP 342 Rhodococcus sp. RHA1
YP_765916    302 GNnADLTEVMALAaeGKIQHTIKTIsf---dDINEYIDLMRDNKIVGRAVVTF 351 Rhizobium leguminosarum bv. viciae 3841
YP_001540737 299 GNlSDFMSVMRLAdsGKIRPLVTKVmr--leEANEALDNLRYARVTARQVLVP 349 Caldivirga maquilingensis IC-167
YP_001540992 292 GSiNEMEEMVKFIkdHGVKSYIEKIpls-egDVNDALVKLSEGKVLGRFVITP 343 Caldivirga maquilingensis IC-167
YP_002565402 297 GRyAELQELVALVeqGEVDLHTSRYdl---gEVNTVAEKLEHGEIDGRAVITP 346 Halorubrum lacusprofundi ATCC 49239

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