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(-) Description

Title :  CRYSTAL STRUCTURE OF ALCOHOL DEHYDROGENASE (TM0436) FROM THERMOTOGA MARITIMA AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 Dec 03  (Deposition) - 02 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tm0436, Alcohol Dehydrogenase, Zinc-Containing, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Alcohol Dehydrogenase (Tm0436) From Thermotoga Maritima At 2. 00 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALCOHOL DEHYDROGENASE, ZINC-CONTAINING
    Chains: A, B, C, D
    EC Number: 1.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0436
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1UNL4Ligand/IonUNKNOWN LIGAND
2ZN8Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:100 , CYS A:103 , CYS A:106 , CYS A:115BINDING SITE FOR RESIDUE ZN A 400
02AC2SOFTWARECYS A:43 , HIS A:65 , GLU A:66 , CYS A:166BINDING SITE FOR RESIDUE ZN A 401
03AC3SOFTWARECYS B:100 , CYS B:103 , CYS B:106 , CYS B:115BINDING SITE FOR RESIDUE ZN B 400
04AC4SOFTWARECYS B:43 , HIS B:65 , GLU B:66 , CYS B:166BINDING SITE FOR RESIDUE ZN B 401
05AC5SOFTWARECYS C:100 , CYS C:103 , CYS C:106 , CYS C:115BINDING SITE FOR RESIDUE ZN C 400
06AC6SOFTWARECYS C:43 , HIS C:65 , GLU C:66 , CYS C:166BINDING SITE FOR RESIDUE ZN C 401
07AC7SOFTWARECYS D:100 , CYS D:103 , CYS D:106 , CYS D:115BINDING SITE FOR RESIDUE ZN D 400
08AC8SOFTWARECYS D:43 , HIS D:65 , GLU D:66 , CYS D:166BINDING SITE FOR RESIDUE ZN D 401
09AC9SOFTWAREARG A:56 , ARG A:96 , ARG A:118 , VAL A:314 , HOH A:2182BINDING SITE FOR RESIDUE UNL A 2001
10BC1SOFTWAREARG B:56 , ARG B:96 , ARG B:118 , VAL B:314 , HOH B:2107BINDING SITE FOR RESIDUE UNL B 2002
11BC2SOFTWAREARG C:56 , ARG C:96 , ARG C:118 , VAL C:314BINDING SITE FOR RESIDUE UNL C 2003
12BC3SOFTWAREARG D:56 , ARG D:96 , ARG D:118BINDING SITE FOR RESIDUE UNL D 2004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VJ0)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Leu A:59 -Pro A:60
2Tyr A:130 -Pro A:131
3Leu B:59 -Pro B:60
4Tyr B:130 -Pro B:131
5Leu C:59 -Pro C:60
6Tyr C:130 -Pro C:131
7Leu D:59 -Pro D:60
8Tyr D:130 -Pro D:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VJ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VJ0)

(-) Exons   (0, 0)

(no "Exon" information available for 1VJ0)

(-) 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:366
 aligned with Q9WYR7_THEMA | Q9WYR7 from UniProtKB/TrEMBL  Length:368

    Alignment length:366
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      
         Q9WYR7_THEMA     2 MGLKAHAMVLEKFNQPLVYKEFEISDIPRGSILVEILSAGVCGSDVHMFRGEDPRVPLPIILGHEGAGRVVEVNGEKRDLNGELLKPGDLIVWNRGITCGECYWCKVSKEPYLCPNRKVYGINRGCSEYPHLRGCYSSHIVLDPETDVLKVSEKDDLDVLAMAMCSGATAYHAFDEYPESFAGKTVVIQGAGPLGLFGVVIARSLGAENVIVIAGSPNRLKLAEEIGADLTLNRRETSVEERRKAIMDITHGRGADFILEATGDSRALLEGSELLRRGGFYSVAGVAVPQDPVPFKVYEWLVLKNATFKGIWVSDTSHFVKTVSITSRNYQLLSKLITHRLPLKEANKALELMESREALKVILYPE 367
               SCOP domains d1vj0a1 A:2-155,A:338-367 Hypothetical protein TM0436                                                                                                     d1vj0a2 A:156-337 Hypothetical protein TM0436                                                                                                                                         d1vj0a1 A:2-155,A:338-367      SCOP domains
               CATH domains 1vj0A01 A:2-166,A:314-367 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                      1vj0A02 A:167-313 NAD(P)-binding Rossmann-like Domain                                                                                              1vj0A01 A:2-166,A:314-367                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee........eeeeeee.......eeeeeeeeeehhhhhhhhh..............eeeeeeeee................eeee..ee....hhhhhh..hhhhh...ee...................eeee.....eeee....hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhh....eeeeee.....hhhhhhhhheeeeeeeee.........eeehhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vj0 A   2 MGLKAHAMVLEKFNQPLVYKEFEISDIPRGSILVEILSAGVCGSDVHMFRGEDPRVPLPIILGHEGAGRVVEVNGEKRDLNGELLKPGDLIVWNRGITCGECYWCKVSKEPYLCPNRKVYGINRGCSEYPHLRGCYSSHIVLDPETDVLKVSEKDDLDVLAMAMCSGATAYHAFDEYPESFAGKTVVIQGAGPLGLFGVVIARSLGAENVIVIAGSPNRLKLAEEIGADLTLNRRETSVEERRKAIMDITHGRGADFILEATGDSRALLEGSELLRRGGFYSVAGVAVPQDPVPFKVYEWLVLKNATFKGIWVSDTSHFVKTVSITSRNYQLLSKLITHRLPLKEANKALELMESREALKVILYPE 367
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      


Chain B from PDB  Type:PROTEIN  Length:364
 aligned with Q9WYR7_THEMA | Q9WYR7 from UniProtKB/TrEMBL  Length:368

    Alignment length:364
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    
         Q9WYR7_THEMA     4 LKAHAMVLEKFNQPLVYKEFEISDIPRGSILVEILSAGVCGSDVHMFRGEDPRVPLPIILGHEGAGRVVEVNGEKRDLNGELLKPGDLIVWNRGITCGECYWCKVSKEPYLCPNRKVYGINRGCSEYPHLRGCYSSHIVLDPETDVLKVSEKDDLDVLAMAMCSGATAYHAFDEYPESFAGKTVVIQGAGPLGLFGVVIARSLGAENVIVIAGSPNRLKLAEEIGADLTLNRRETSVEERRKAIMDITHGRGADFILEATGDSRALLEGSELLRRGGFYSVAGVAVPQDPVPFKVYEWLVLKNATFKGIWVSDTSHFVKTVSITSRNYQLLSKLITHRLPLKEANKALELMESREALKVILYPE 367
               SCOP domains d1vj0b1 B:4-155,B:338-367 Hypothetical protein TM0436                                                                                                   d1vj0b2 B:156-337 Hypothetical protein TM0436                                                                                                                                         d1vj0b1 B:4-155,B:338-367      SCOP domains
               CATH domains 1vj0B01 B:4-166,B:314-367 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                    1vj0B02 B:167-313 NAD(P)-binding Rossmann-like Domain                                                                                              1vj0B01 B:4-166,B:314-367                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeee........eeeeeeeeeehhhhhhhhh.........ee....eeeeeeee................eeee..ee....hhhhhh..hhhhh...ee...................eeee.....eeee....hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhh....eeeeee.....hhhhhhhhheeeeeeeee.........eeehhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vj0 B   4 LKAHAMVLEKFNQPLVYKEFEISDIPRGSILVEILSAGVCGSDVHMFRGEDPRVPLPIILGHEGAGRVVEVNGEKRDLNGELLKPGDLIVWNRGITCGECYWCKVSKEPYLCPNRKVYGINRGCSEYPHLRGCYSSHIVLDPETDVLKVSEKDDLDVLAMAMCSGATAYHAFDEYPESFAGKTVVIQGAGPLGLFGVVIARSLGAENVIVIAGSPNRLKLAEEIGADLTLNRRETSVEERRKAIMDITHGRGADFILEATGDSRALLEGSELLRRGGFYSVAGVAVPQDPVPFKVYEWLVLKNATFKGIWVSDTSHFVKTVSITSRNYQLLSKLITHRLPLKEANKALELMESREALKVILYPE 367
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    


Chain C from PDB  Type:PROTEIN  Length:364
 aligned with Q9WYR7_THEMA | Q9WYR7 from UniProtKB/TrEMBL  Length:368

    Alignment length:364
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    
         Q9WYR7_THEMA     4 LKAHAMVLEKFNQPLVYKEFEISDIPRGSILVEILSAGVCGSDVHMFRGEDPRVPLPIILGHEGAGRVVEVNGEKRDLNGELLKPGDLIVWNRGITCGECYWCKVSKEPYLCPNRKVYGINRGCSEYPHLRGCYSSHIVLDPETDVLKVSEKDDLDVLAMAMCSGATAYHAFDEYPESFAGKTVVIQGAGPLGLFGVVIARSLGAENVIVIAGSPNRLKLAEEIGADLTLNRRETSVEERRKAIMDITHGRGADFILEATGDSRALLEGSELLRRGGFYSVAGVAVPQDPVPFKVYEWLVLKNATFKGIWVSDTSHFVKTVSITSRNYQLLSKLITHRLPLKEANKALELMESREALKVILYPE 367
               SCOP domains d1vj0c1 C:4-155,C:338-367 Hypothetical protein TM0436                                                                                                   d1vj0c2 C:156-337 Hypothetical protein TM0436                                                                                                                                         d1vj0c1 C:4-155,C:338-367      SCOP domains
               CATH domains 1vj0C01 C:4-166,C:314-367 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                    1vj0C02 C:167-313 NAD(P)-binding Rossmann-like Domain                                                                                              1vj0C01 C:4-166,C:314-367                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeee........eeeeeeeeeehhhhhhhhh.........ee...eeeeeeeee................eeee..ee....hhhhhh..hhhhh...ee...................eeee.....eeee....hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhh....eeeeee.....hhhhhhhhheeeeeeeee.........eeehhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vj0 C   4 LKAHAMVLEKFNQPLVYKEFEISDIPRGSILVEILSAGVCGSDVHMFRGEDPRVPLPIILGHEGAGRVVEVNGEKRDLNGELLKPGDLIVWNRGITCGECYWCKVSKEPYLCPNRKVYGINRGCSEYPHLRGCYSSHIVLDPETDVLKVSEKDDLDVLAMAMCSGATAYHAFDEYPESFAGKTVVIQGAGPLGLFGVVIARSLGAENVIVIAGSPNRLKLAEEIGADLTLNRRETSVEERRKAIMDITHGRGADFILEATGDSRALLEGSELLRRGGFYSVAGVAVPQDPVPFKVYEWLVLKNATFKGIWVSDTSHFVKTVSITSRNYQLLSKLITHRLPLKEANKALELMESREALKVILYPE 367
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    


Chain D from PDB  Type:PROTEIN  Length:365
 aligned with Q9WYR7_THEMA | Q9WYR7 from UniProtKB/TrEMBL  Length:368

    Alignment length:365
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362     
         Q9WYR7_THEMA     3 GLKAHAMVLEKFNQPLVYKEFEISDIPRGSILVEILSAGVCGSDVHMFRGEDPRVPLPIILGHEGAGRVVEVNGEKRDLNGELLKPGDLIVWNRGITCGECYWCKVSKEPYLCPNRKVYGINRGCSEYPHLRGCYSSHIVLDPETDVLKVSEKDDLDVLAMAMCSGATAYHAFDEYPESFAGKTVVIQGAGPLGLFGVVIARSLGAENVIVIAGSPNRLKLAEEIGADLTLNRRETSVEERRKAIMDITHGRGADFILEATGDSRALLEGSELLRRGGFYSVAGVAVPQDPVPFKVYEWLVLKNATFKGIWVSDTSHFVKTVSITSRNYQLLSKLITHRLPLKEANKALELMESREALKVILYPE 367
               SCOP domains d1vj0d1 D:3-155,D:338-367 Hypothetical protein TM0436                                                                                                    d1vj0d2 D:156-337 Hypothetical protein TM0436                                                                                                                                         d1vj0d1 D:3-155,D:338-367      SCOP domains
               CATH domains 1vj0D01 D:3-166,D:314-367 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                     1vj0D02 D:167-313 NAD(P)-binding Rossmann-like Domain                                                                                              1vj0D01 D:3-166,D:314-367                              CATH domains
           Pfam domains (1) ---------------------------ADH_N-1vj0D01 D:30-152                                                                                                     -----------------------------------------ADH_zinc_N-1vj0D05 D:194-326                                                                                                         ----------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------ADH_N-1vj0D02 D:30-152                                                                                                     -----------------------------------------ADH_zinc_N-1vj0D06 D:194-326                                                                                                         ----------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------ADH_N-1vj0D03 D:30-152                                                                                                     -----------------------------------------ADH_zinc_N-1vj0D07 D:194-326                                                                                                         ----------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------ADH_N-1vj0D04 D:30-152                                                                                                     -----------------------------------------ADH_zinc_N-1vj0D08 D:194-326                                                                                                         ----------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeeee........eeeeeee.......eeeeeeeeeehhhhhhhhh..............eeeeeeeee................eeee..ee....hhhhhh..hhhhh...ee...................eeee.....eeee....hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhh....eeeeee.....hhhhhhhhheeeeeeeee.........eeehhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vj0 D   3 GLKAHAMVLEKFNQPLVYKEFEISDIPRGSILVEILSAGVCGSDVHMFRGEDPRVPLPIILGHEGAGRVVEVNGEKRDLNGELLKPGDLIVWNRGITCGECYWCKVSKEPYLCPNRKVYGINRGCSEYPHLRGCYSSHIVLDPETDVLKVSEKDDLDVLAMAMCSGATAYHAFDEYPESFAGKTVVIQGAGPLGLFGVVIARSLGAENVIVIAGSPNRLKLAEEIGADLTLNRRETSVEERRKAIMDITHGRGADFILEATGDSRALLEGSELLRRGGFYSVAGVAVPQDPVPFKVYEWLVLKNATFKGIWVSDTSHFVKTVSITSRNYQLLSKLITHRLPLKEANKALELMESREALKVILYPE 367
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: GroES (70)
(-)
Family: ADH_N (62)
(-)
Thermotoga maritima (1)
1aADH_N-1vj0D01D:30-152
1bADH_N-1vj0D02D:30-152
1cADH_N-1vj0D03D:30-152
1dADH_N-1vj0D04D:30-152
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9WYR7_THEMA | Q9WYR7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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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