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(-) Description

Title :  ALCOHOL DEHYDROGENASE FROM CLOSTRIDIUM BEIJERINCKII: CRYSTAL STRUCTURE OF MUTANT WITH ENHANCED THERMAL STABILITY
 
Authors :  I. Levin, F. Frolow, O. Bogin, M. Peretz, Y. Hacham, Y. Burstein
Date :  05 Aug 01  (Deposition) - 13 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tetramer Of 222 Symmetry, Water-Mediated Intersubunit Salt Bridges, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Bogin, I. Levin, Y. Hacham, S. Tel-Or, M. Peretz, F. Frolow, Y. Burstein
Structural Basis For The Enhanced Thermal Stability Of Alcohol Dehydrogenase Mutants From The Mesophilic Bacterium Clostridium Beijerinckii: Contribution Of Salt Bridging
Protein Sci. V. 11 2561 2002
PubMed-ID: 12381840  |  Reference-DOI: 10.1110/PS.0222102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NADP-DEPENDENT ALCOHOL DEHYDROGENASE
    ChainsA, B, C, D
    EC Number1.1.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBS-P200
    Expression System StrainTG2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificCLOSTRIDIUM BEIJERINCKII
    Organism Taxid1520

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1037 , HIS A:1059 , ASP A:1150BINDING SITE FOR RESIDUE ZN A 1353
2AC2SOFTWARECYS B:2037 , HIS B:2059 , GLU B:2060 , ASP B:2150BINDING SITE FOR RESIDUE ZN B 2353
3AC3SOFTWARECYS C:3037 , HIS C:3059 , ASP C:3150BINDING SITE FOR RESIDUE ZN C 3353
4AC4SOFTWAREHOH D:112 , CYS D:4037 , HIS D:4059 , ASP D:4150BINDING SITE FOR RESIDUE ZN D 4353

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JQB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_ZINCPS00059 Zinc-containing alcohol dehydrogenases signature.ADH_CLOBE58-72
 
 
 
  4A:1058-1072
B:2058-2072
C:3058-3072
D:4058-4072

(-) Exons   (0, 0)

(no "Exon" information available for 1JQB)

(-) 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:351
 aligned with ADH_CLOBE | P25984 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:351
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
           ADH_CLOBE      1 MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFQQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIQMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIVDQVMKLTNGKGVDRVIMAGGGSETLSQAVSMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAEMLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL  351
               SCOP domains d1jqba1 A:1001-1139,A:1314-1351 Bacterial secondary alcohol dehydrogenase                                                                  d1jqba2 A:1140-1313 Bacterial secondary alcohol dehydrogenase                                                                                                                 d1jqba1 A:1001-1139,A:1314-1351        SCOP domains
               CATH domains 1jqbA01 A:1001-1154,A:1293-1351 Medium-chain alcohol dehydrogenases, catalytic domain                                                                     1jqbA02 A:1155-1292 NAD(P)-binding Rossmann-like Domain                                                                                   1jqbA01 A:1001-1154,A:1293-1351                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee..........eeeeeeee..hhhhhhhhhhh.......ee....eeeeeeee...........eeee........hhhhhh.hhhhh....................eee.hhhhhhee.....hhhhhhh..hhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh..eeehhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhheeeeeeeee........eeeee...hhhhh...eeee....hhhhhhhhhhhhhhh...hhhh.eeeeee...hhhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------ADH_ZINC       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jqb A 1001 MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFQQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIEMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIEDQVMKLTNGKGVDRVIMAGGGSETLSQAVKMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAERLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL 1351
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350 

Chain B from PDB  Type:PROTEIN  Length:351
 aligned with ADH_CLOBE | P25984 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:351
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
           ADH_CLOBE      1 MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFQQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIQMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIVDQVMKLTNGKGVDRVIMAGGGSETLSQAVSMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAEMLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL  351
               SCOP domains d1jqbb1 B:2001-2139,B:2314-2351 Bacterial secondary alcohol dehydrogenase                                                                  d1jqbb2 B:2140-2313 Bacterial secondary alcohol dehydrogenase                                                                                                                 d1jqbb1 B:2001-2139,B:2314-2351        SCOP domains
               CATH domains 1jqbB01 B:2001-2154,B:2293-2351 Medium-chain alcohol dehydrogenases, catalytic domain                                                                     1jqbB02 B:2155-2292 NAD(P)-binding Rossmann-like Domain                                                                                   1jqbB01 B:2001-2154,B:2293-2351                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee..........eeeeeeee..hhhhhhhhhh........ee....eeeeeeee...........eeee........hhhhhh.hhhhh....................eee.hhhhhhee.....hhhhhhh..hhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh..eeehhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhheeeeeeeee........eeeee...hhhhh...eeee....hhhhhhhhhhhhhhh...hhhh.eeeee.hhhhhhhhhhhh........eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------ADH_ZINC       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jqb B 2001 MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFQQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIEMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIEDQVMKLTNGKGVDRVIMAGGGSETLSQAVKMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAERLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL 2351
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210      2220      2230      2240      2250      2260      2270      2280      2290      2300      2310      2320      2330      2340      2350 

Chain C from PDB  Type:PROTEIN  Length:351
 aligned with ADH_CLOBE | P25984 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:351
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
           ADH_CLOBE      1 MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFQQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIQMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIVDQVMKLTNGKGVDRVIMAGGGSETLSQAVSMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAEMLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL  351
               SCOP domains d1jqbc1 C:3001-3139,C:3314-3351 Bacterial secondary alcohol dehydrogenase                                                                  d1jqbc2 C:3140-3313 Bacterial secondary alcohol dehydrogenase                                                                                                                 d1jqbc1 C:3001-3139,C:3314-3351        SCOP domains
               CATH domains 1jqbC01 C:3001-3154,C:3293-3351 Medium-chain alcohol dehydrogenases, catalytic domain                                                                     1jqbC02 C:3155-3292 NAD(P)-binding Rossmann-like Domain                                                                                   1jqbC01 C:3001-3154,C:3293-3351                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....eee............eeeeeeee..hhhhhhhhhh........ee....eeeeeeee...........eeee........hhhhhh.hhhhh....................eee.hhhhhhee.....hhhhhhhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhh.....eeee..hhhhhhhhhhh...eeehhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhheeeeeeeee........eeeee...hhhhh...eeee.....hhhhhhhhhhhhhh...hhhh.eeeeee...hhhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------ADH_ZINC       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jqb C 3001 MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFQQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIEMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIEDQVMKLTNGKGVDRVIMAGGGSETLSQAVKMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAERLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL 3351
                                  3010      3020      3030      3040      3050      3060      3070      3080      3090      3100      3110      3120      3130      3140      3150      3160      3170      3180      3190      3200      3210      3220      3230      3240      3250      3260      3270      3280      3290      3300      3310      3320      3330      3340      3350 

Chain D from PDB  Type:PROTEIN  Length:351
 aligned with ADH_CLOBE | P25984 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:351
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
           ADH_CLOBE      1 MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFQQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIQMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIVDQVMKLTNGKGVDRVIMAGGGSETLSQAVSMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAEMLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL  351
               SCOP domains d1jqbd1 D:4001-4139,D:4314-4351 Bacterial secondary alcohol dehydrogenase                                                                  d1jqbd2 D:4140-4313 Bacterial secondary alcohol dehydrogenase                                                                                                                 d1jqbd1 D:4001-4139,D:4314-4351        SCOP domains
               CATH domains 1jqbD01 D:4001-4154,D:4293-4351 Medium-chain alcohol dehydrogenases, catalytic domain                                                                     1jqbD02 D:4155-4292 NAD(P)-binding Rossmann-like Domain                                                                                   1jqbD01 D:4001-4154,D:4293-4351                             CATH domains
           Pfam domains (1) -----------------------ADH_N-1jqbD01 D:4024-4134                                                                                      ------------------------------------------ADH_zinc_N-1jqbD05 D:4177-4309                                                                                                       ------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------ADH_N-1jqbD02 D:4024-4134                                                                                      ------------------------------------------ADH_zinc_N-1jqbD06 D:4177-4309                                                                                                       ------------------------------------------ Pfam domains (2)
           Pfam domains (3) -----------------------ADH_N-1jqbD03 D:4024-4134                                                                                      ------------------------------------------ADH_zinc_N-1jqbD07 D:4177-4309                                                                                                       ------------------------------------------ Pfam domains (3)
           Pfam domains (4) -----------------------ADH_N-1jqbD04 D:4024-4134                                                                                      ------------------------------------------ADH_zinc_N-1jqbD08 D:4177-4309                                                                                                       ------------------------------------------ Pfam domains (4)
         Sec.struct. author .eeeee.....eeeee..........eeeeeeee...hhhhhhhhh........ee....eeeeeeee...........eeee........hhhhhh.hhhhh....................eee.hhhhhhee.....hhhhhhh..hhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh..eee.....hhhhhhhhhh....eeeeee.....hhhhhhhhheeeeeeeee........eeeee.hhhhhhh...eeee.....hhhhhhhhhhhhhh...hhhh.eeeeee...hhhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------ADH_ZINC       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jqb D 4001 MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFQQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIEMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIEDQVMKLTNGKGVDRVIMAGGGSETLSQAVKMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAERLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL 4351
                                  4010      4020      4030      4040      4050      4060      4070      4080      4090      4100      4110      4120      4130      4140      4150      4160      4170      4180      4190      4200      4210      4220      4230      4240      4250      4260      4270      4280      4290      4300      4310      4320      4330      4340      4350 

   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
1ad1jqba1A:1001-1139,A:1314-1351
1bd1jqbb1B:2001-2139,B:2314-2351
1cd1jqbc1C:3001-3139,C:3314-3351
1dd1jqbd1D:4001-4139,D:4314-4351

(-) 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)
1aADH_N-1jqbD01D:4024-4134
1bADH_N-1jqbD02D:4024-4134
1cADH_N-1jqbD03D:4024-4134
1dADH_N-1jqbD04D:4024-4134

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (ADH_CLOBE | P25984)
molecular function
    GO:0050009    isopropanol dehydrogenase (NADP+) activity    Catalysis of the reaction: NADP(+) + propan-2-ol = acetone + H(+) + NADPH.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ADH_CLOBE | P259841kev 1ped 2b83 3fpl 3fsr 3ftn

(-) Related Entries Specified in the PDB File

1kev 1KEV CONTAINS WILD-TYPE STRUCTURE OF ALCOHOL DEHYDROGENASE FROM CLOSTRIDIUM BEIJERINCKII