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(-) Description

Title :  CRYSTAL STRUCTURE OF AN IRON CONTAINING ALCOHOL DEHYDROGENASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - ALCOHOL DEHYDROGENASE, IRON-CONTAINING
    Chains: A, B
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GBSB
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 28)

Asymmetric/Biological Unit (4, 28)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2MSE22Mod. Amino AcidSELENOMETHIONINE
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:116 , LEU A:119 , TYR A:120 , SER A:148 , LEU A:150 , ARG A:158 , CYS A:160BINDING SITE FOR RESIDUE CAC A 370
2AC2SOFTWARELEU B:119 , TYR B:120 , SER B:148 , LEU B:150 , ARG B:158 , CYS B:160BINDING SITE FOR RESIDUE CAC B 370
3AC3SOFTWAREASP A:189 , HIS A:193 , HIS A:256 , HIS A:270 , NAP A:372 , HOH A:611BINDING SITE FOR RESIDUE ZN A 371
4AC4SOFTWAREASP B:189 , HIS B:193 , HIS B:256 , HIS B:270 , NAP B:372 , HOH B:517BINDING SITE FOR RESIDUE ZN B 371
5AC5SOFTWAREGLY A:36 , SER A:38 , SER A:39 , ASN A:43 , GLU A:68 , ASN A:69 , GLY A:95 , GLY A:96 , SER A:97 , PRO A:98 , ASP A:100 , THR A:136 , THR A:137 , THR A:140 , SER A:142 , THR A:145 , TYR A:147 , LYS A:157 , TYR A:174 , SER A:177 , MSE A:178 , LEU A:182 , THR A:186 , ASP A:189 , HIS A:193 , HIS A:270 , ZN A:371 , HOH A:389 , HOH A:420 , HOH A:427 , HOH A:455 , HOH A:473 , HOH A:483 , HOH A:540 , HOH A:569 , HOH A:570 , HOH A:571 , HOH A:610 , HOH A:611 , HOH A:704BINDING SITE FOR RESIDUE NAP A 372
6AC6SOFTWAREGLY B:36 , LYS B:37 , SER B:38 , SER B:39 , ASN B:43 , GLU B:68 , ASN B:69 , GLY B:95 , GLY B:96 , SER B:97 , PRO B:98 , ASP B:100 , THR B:136 , THR B:137 , THR B:140 , SER B:142 , THR B:145 , TYR B:147 , ILE B:149 , TYR B:174 , SER B:177 , MSE B:178 , LEU B:182 , THR B:186 , ASP B:189 , HIS B:193 , HIS B:270 , ZN B:371 , HOH B:410 , HOH B:423 , HOH B:445 , HOH B:447 , HOH B:488 , HOH B:489 , HOH B:507 , HOH B:517 , HOH B:538 , HOH B:551 , HOH B:587BINDING SITE FOR RESIDUE NAP B 372

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VHD)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:138 -Gly A:139
2Ala B:138 -Gly B:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VHD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VHD)

(-) Exons   (0, 0)

(no "Exon" information available for 1VHD)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:361
 aligned with Q9X022_THEMA | Q9X022 from UniProtKB/TrEMBL  Length:359

    Alignment length:361
                             1                                                                                                                                                                                                                                                                                                                                                                   359 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359 
         Q9X022_THEMA     - -MWEFYMPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISYEIFDEVEENPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTTAGTGSEVTPYSILTDPEGNKRGCTLMFPVYAFLDPRYTYSMSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAMKIIHRNLPKAIEGNREARKKMFVASCLAGMVIAQTGTTLAHALGYPLTTEKGIKHGKATGMVLPFVMEVMKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALGV-   -
               SCOP domains d1vhda_ A: Alcohol dehydrogenase TM0920                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------1vhdA01 A:7-179  [code=3.40.50.1970, no name defined]                                                                                                                        1vhdA02 A:180-359 Dehydroquinate synthase-like - alpha domain                                                                                                                       - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....eeee..hhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh......hhhhhhhhhh.....eeeee.....hhhhh.eeeee.....eeeee.....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhd A   0 SLWEFYmPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISYEIFDEVEENPSFDNVmKAVERYRNDSFDFVVGLGGGSPmDFAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTTAGTGSEVTPYSILTDPEGNKRGCTLmFPVYAFLDPRYTYSmSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAmKIIHRNLPKAIEGNREARKKmFVASCLAGmVIAQTGTTLAHALGYPLTTEKGIKHGKATGmVLPFVmEVmKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALGVE 360
                                  |  9        19        29        39        49        59        69      | 79        89        99       109       119       129       139       149       159   |   169       179       189       199       209     | 219       229      |239     | 249       259       269      |279  |  | 289       299       309       319       329       339       349       359 
                                  6-MSE                                                                76-MSE                 99-MSE                                                         163-MSE        178-MSE                              215-MSE              236-MSE  245-MSE                        276-MSE |  |                                                                           
                                                                                                                                                                                                                                                                                                                    282-MSE                                                                          
                                                                                                                                                                                                                                                                                                                       285-MSE                                                                       


Chain B from PDB  Type:PROTEIN  Length:361
 aligned with Q9X022_THEMA | Q9X022 from UniProtKB/TrEMBL  Length:359

    Alignment length:361
                             1                                                                                                                                                                                                                                                                                                                                                                   359 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359 
         Q9X022_THEMA     - -MWEFYMPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISYEIFDEVEENPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTTAGTGSEVTPYSILTDPEGNKRGCTLMFPVYAFLDPRYTYSMSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAMKIIHRNLPKAIEGNREARKKMFVASCLAGMVIAQTGTTLAHALGYPLTTEKGIKHGKATGMVLPFVMEVMKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALGV-   -
               SCOP domains d1vhdb_ B: Alcohol dehydrogenase TM0920                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------1vhdB01 B:7-179  [code=3.40.50.1970, no name defined]                                                                                                                        1vhdB02 B:180-359 Dehydroquinate synthase-like - alpha domain                                                                                                                       - CATH domains
           Pfam domains (1) -------Fe-ADH-1vhdB01 B:7-349                                                                                                                                                                                                                                                                                                                                 ----------- Pfam domains (1)
           Pfam domains (2) -------Fe-ADH-1vhdB02 B:7-349                                                                                                                                                                                                                                                                                                                                 ----------- Pfam domains (2)
         Sec.struct. author ..eee....eeeee.hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh......hhhhhh.........eeeee.....hhhhh.eeeee.....eeeee.....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhd B   0 SLWEFYmPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISYEIFDEVEENPSFDNVmKAVERYRNDSFDFVVGLGGGSPmDFAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTTAGTGSEVTPYSILTDPEGNKRGCTLmFPVYAFLDPRYTYSmSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAmKIIHRNLPKAIEGNREARKKmFVASCLAGmVIAQTGTTLAHALGYPLTTEKGIKHGKATGmVLPFVmEVmKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALGVE 360
                                  |  9        19        29        39        49        59        69      | 79        89        99       109       119       129       139       149       159   |   169       179       189       199       209     | 219       229      |239     | 249       259       269      |279  |  | 289       299       309       319       329       339       349       359 
                                  6-MSE                                                                76-MSE                 99-MSE                                                         163-MSE        178-MSE                              215-MSE              236-MSE  245-MSE                        276-MSE |  |                                                                           
                                                                                                                                                                                                                                                                                                                    282-MSE                                                                          
                                                                                                                                                                                                                                                                                                                       285-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DHQS (27)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9X022_THEMA | Q9X022)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  1vhd
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  Q9X022_THEMA | Q9X022
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9X022_THEMA | Q9X022: 1o2d

(-) Related Entries Specified in the PDB File

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