3FBG


Conserved Protein Domain Family
AL_MDR

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cd08252: AL_MDR 
Click on image for an interactive view with Cn3D
Arginate lyase and other MDR family members
This group contains a structure identified as an arginate lyase. Other members are identified quinone reductases, alginate lyases, and other proteins related to the zinc-dependent dehydrogenases/reductases. QOR catalyzes the conversion of a quinone and NAD(P)H to a hydroquinone and NAD(P+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR acts in 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. 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. 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: 176214
View PSSM: cd08252
Aligned: 53 rows
Threshold Bit Score: 344.894
Threshold Setting Gi: 219125185
Created: 24-Apr-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
putative NAD(P)dimer interface
Conserved site includes 24 residues -Click on image for an interactive view with Cn3D
Feature 1:putative NAD(P) binding site [chemical binding site]
Evidence:
  • Comment:MDR family binds NAD(P) as a cofactor
  • Comment:defined by comparison to MDR alcohol dehydrogenase like family

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                   ###  #                               
3FBG_A         3 LKAIGFEQPFKLsdgnlFKTFNLDIPEPk-vHEILVKIQSISVNPVDTKQRLmdv----------skaPRVLGFDAIGVV 71  Staphylococcus ...
XP_001401178   1 MKAIGVENYGPVd---rLEAWEVPKPTDlqpRDLLVRIKGVAVNPVDTKVRNdyydr-------vprpFQITGYDASGIV 70  Aspergillus nig...
XP_001470816   9 IKAIGLTDPKGD-----LQLIQIPIKTLg-pQDILIRVEAISINPLDYKWAQhmrtqn-----isessPAIFGYDASGVV 77  Tetrahymena the...
NP_785816      3 AKAVGLTQGLPVsdpnsLQDVTINVNQPr-gRDILVAVLATAVNPIDTKQRQgqsp---------vttPRILGFDAVAKV 72  Lactobacillus p...
YP_163786      1 MKAIGFTQHLNIndsrsLFEFEESIPVPk-gHDLLVKVNAVSVNPVDVGVRRgghg--------klktPKVIGWDACGIV 71  Lactobacillus s...
YP_818660     19 MRAIGFERPLLIdqpdaFVEKVIPRPQPd-kDELLVKVLASSVNPVDTKMRAnyth---------dgvFRILGFDAVGVV 88  Leuconostoc mes...
YP_794919      4 MHAIGFDRHLPIednhsFFDVTVPRPEPt-gHDLLVQIIATSVNPVDTAVRRntvg--------ilehPKVIGWDAYGIV 74  Lactobacillus b...
YP_395617      5 NKAVGFYKHLPIsnpdsFEDIMCQLPTIg-dHDLLVKVEGVSVNPVDTFVRCsgrst-------kmahPKVIGWDAVGTV 76  Lactobacillus s...
XP_001940450   1 MHAIAVTEYGPIt---nLKTLDLPKPSDpqgHDILVRVKACSVNPVDTKVRAgtyddypdyyertpklPQILGFDGAGVI 77  Pyrenophora tri...
NP_266873      1 MKAIGTIDSSKN-----FIDFEIEKPILr-pHDLLIKVEAISINPVDTKVRKgikg--------nlaePKILGWDGLGTV 66  Lactococcus lac...
Feature 1                                                               #   #                    
3FBG_A        72 ESVGNEVTMFNQGDIVYYSGSPDQNGSNAEYQLINERLVAKAPKNISAEQAVSLPLTGITAYETLFDVfgisrnr-nene 150 Staphylococcus ...
XP_001401178  71 EATGSQCSLFNVGDEVYYSGSPIRQGSNAEYQLVDERSVGRKPKSLDFVESAAMPLTYITAYEALVERleiek-----ee 145 Aspergillus nig...
XP_001470816  78 VQTGSDCRLFKVGDQVIYSGDFTKLGSNSNYQIVDERLAGKKPQKLTHPEAAAIPLVALTAYEALVEElgileinkiqnq 157 Tetrahymena the...
NP_785816     73 LAVGEAVTTIMTDDVVYYAGAVDRPGSDAQYQLVDERLVACAPKTWSPAQSAGLPLTTLTAWEALFEKlpftaaa-danl 151 Lactobacillus p...
YP_163786     72 KKVGNQVSLFNPGDRVYYAGSFKRPGSNSEYQLVDERIVGHAPKSLSDDEAAAMPLTSLTAYEALFEQlsvssns-qsnk 150 Lactobacillus s...
YP_818660     89 VEVGQNVQHFSVGDKVYYAGAQLKPGSNADLQVVHEALVGHAPTSLSDEEIAAMPLTSITAYEILHEAlcydlee-nsal 167 Leuconostoc mes...
YP_794919     75 TAVGNDVHDFQSGDRVFYAGSFKRSGTDSDYQLVDERIVGHVPTSLSPAEIAAMPLTSLTAWEALFEQmhldidhpadna 154 Lactobacillus b...
YP_395617     77 VEVGSECTLFKPNDQVWYAGDFKRSGSDSQYQSVDERIVGPTPQNLSLQEAAAIPLVGLTVYESLFEKlalswdi-lknk 155 Lactobacillus s...
XP_001940450  78 ESVGSEVINFKPCDEIYYAGSPIRQGSNAEFQLVDSRVVALKPKSLDWGQAAAMPLTWITAYEALVERmeiqk-----ge 152 Pyrenophora tri...
NP_266873     67 VELGSETKLFKVGDKVFWAGDVTRSGSNAEFQAVDERIVGFAPKNLTKEKAVAMPLTSLTAYELLFEKlevtd----ksk 142 Lactococcus lac...
Feature 1               #### ##                   ##   #               #                      ## 
3FBG_A       151 gkTLLIINGAGGVGSIATQIAKAyg--lrVITTASRNETIEWTKKMGAD-IVLNHKESLLNQFKTqgi-elVDYVFCTFN 226 Staphylococcus ...
XP_001401178 146 kaALLIINGAGGVGAMATQIARVvldlpvVITTASRPETIQFTKDMGAT-HVVNHREDVASQIEKlnlevpLKYIFITHS 224 Aspergillus nig...
XP_001470816 158 skKILIVGGAGGVGSIAIQIAKKilg-ltVITTASRVETINFCKKMGAD-YVINHQNALAEELKKini-esLDYIFNTVD 234 Tetrahymena the...
NP_785816    152 gqSVLIINGAGGVGSMAIQLAKWag--lqVITTTGKPETTEWVKRLGAD-IVLDYHQDLGSQLAAagl-qaVDHAILLHS 227 Lactobacillus p...
YP_163786    151 dkTILIINGAGGVGSVATQLAANag--ltVIATASRPESINWVKSHGAK-YTVNHRNNLVDEVRElgy-kfVDYILELKD 226 Lactobacillus s...
YP_818660    168 ghTILIVNGAGGVGSVLIQLAKYig--mtVITTASRTESVTWVKSLGAD-YILDYHQDLNEQMRKiqh-dkVDNIAILQN 243 Leuconostoc mes...
YP_794919    155 grTLLVINGAGGVGSVATQLAKLag--ltVIATASRPETIAWTKQHGAD-HVVNHRQDVVEQVHAlgl-dtVDYILELSN 230 Lactobacillus b...
YP_395617    156 gkTILIINCAGGVGSMAIQLAKLag--lrVIATASNPDAIAWVNQLKAD-AVIDHHQDLVKQMHHlki-rdVDYILNLNN 231 Lactobacillus s...
XP_001940450 153 naGILIINGAGGVGSVASQIARRvlnlpvVVTTASREETVRFSKHVGGAtHTVNHHQDIAAEVEKlklevpIKYIFITHT 232 Pyrenophora tri...
NP_266873    143 gkSLLIINGAGGVGSVAIQMAKNag--ltVIATASNPQAIEWVKNFGAD-YTVNHHEKLVPQVHElgf-kfVDYILILNA 218 Lactococcus lac...
Feature 1        #                    ##                     ###                                 
3FBG_A       227 Td-mYYDDMIQLVKPRGHIATIVAfe-nDQDLNALKPKSLSFSHEFMFARPLNQTdDMIKHHEYLEDITNKVEQNIYQPT 304 Staphylococcus ...
XP_001401178 225 Td-qYMDTCARVCAPFGKVCSIVQgq-aKMYGTEFMSKSLTFVWCLLGTKPYHKV-DVESHHRILEELTDMIDAGKIKCH 301 Aspergillus nig...
XP_001470816 235 MtqqYFNQFTPLIKPFGHIVGIVGfe-qPLNIQGLFLKRARLSVECIFTRAIFQV-EPERQNQILNKIGDLYDSGIFIST 312 Tetrahymena the...
NP_785816    228 Td-qYLPLVTPLVRPLGTIVAVVTnq-hPLPMALLKPKSLNFAWEFMFTKANYQLpSMATQGSILAQVAQLADAGVIVPT 305 Lactobacillus p...
YP_163786    227 Id-nHWKEMCELIKPEGAIASITEnk-rPINLRLLTQKKAIFAWEWMYTKSYYHTnDMQTQHDILEKIAYFLDNGQLKCT 304 Lactobacillus s...
YP_818660    244 Td-yYWPLATAVIKPFGRIASIVEtt-ePIDMGPLKNIGAQFSWVFMFAKGNYGV-NMQSQGNALNQVARLLDENKIKTT 320 Leuconostoc mes...
YP_794919    231 Ln-qHWSEIVDLIAPSGTIVSITGsn-tPIDLRALKQKRATFAWEWMYTKSFYETpDMQSQHAILERVRGLLDAGRLQST 308 Lactobacillus b...
YP_395617    232 Ld-aHWNEIAEIIKPDGRVTATTEnh-kLIDLQKLTKKRVTFSWEWMYSKSYYQTaDMATQNQILTELCQLFEMKKLMPI 309 Lactobacillus s...
XP_001940450 233 PtsgYLSPAAKICAPFGKVCSIVQdkemPMYGTEFMAKSLTFVWALLGTKPYYGV-DAESHGKILKDLTGMLDDGTIKCH 311 Pyrenophora tri...
NP_266873    219 Vv-eHMPAVNELIAPQGSIANIVEpg-qAINLDQLAHKSARFNFEWMFTKVVSNTsDLQSQHDILNKVSEWLDNDVLKST 296 Lactococcus lac...
Feature 1                                        
3FBG_A       305 TtKVIEGLTtENIYQAHQILESNTMIGKLVIN 336 Staphylococcus haemolyticus JCSC1435
XP_001401178 302 L-TKRLKLTlDGVKKGHELLQSGGSIGKVGLG 332 Aspergillus niger CBS 513.88
XP_001470816 313 V-QIEKPFNlENLLEAHAFSESGKTIGKVVLS 343 Tetrahymena thermophila
NP_785816    306 TkRTLAGINaANLRTAHTIVETGQMLGKIVLT 337 Lactobacillus plantarum WCFS1
YP_163786    305 LtHSLSPLNaTNLRKAHSLVESGHMVGKVVVS 336 Lactobacillus salivarius UCC118
YP_818660    321 LsKTYHGLSvENIRAATKEVEAGRMIGKVVVK 352 Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
YP_794919    309 LtKTLTPITaANLRQAHALVESNRMIGKVVLT 340 Lactobacillus brevis ATCC 367
YP_395617    310 TtKTYTPINaEHLKRAHRDVESGHMIGKVTLT 341 Lactobacillus sakei subsp. sakei 23K
XP_001940450 312 CmQKLKVDE-EGLRKAHEIIEGGKAVGKVALE 342 Pyrenophora tritici-repentis Pt-1C-BFP
NP_266873    297 MtQNLGPITaENVKKAHELIEENHTIGKIILS 328 Lactococcus lactis subsp. lactis Il1403

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