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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BINARY COMPLEX: NADP(H)-DEPENDENT VERTEBRATE ALCOHOL DEHYDROGENASE (ADH8) WITH THE COFACTOR NADP
 
Authors :  A. Rosell, E. Valencia, X. Pares, I. Fita, J. Farres, W. F. Ochoa
Date :  10 Apr 03  (Deposition) - 22 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Adh Topology, Nadp(H)-Dependent, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Rosell, E. Valencia, X. Pares, I. Fita, J. Farres, W. F. Ochoa
Crystal Structure Of The Vertebrate Nadp(H)-Dependent Alcohol Dehydrogenase (Adh8)
J. Mol. Biol. V. 330 75 2003
PubMed-ID: 12818203  |  Reference-DOI: 10.1016/S0022-2836(03)00431-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NADP-DEPENDENT ALCOHOL DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX4T-2
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: ADH
    Organism Common: PEREZ'S FROG
    Organism Scientific: RANA PEREZI
    Organism Taxid: 8403

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1046 , HIS A:1067 , CYS A:1173 , NAP A:4292 , GOL A:8001BINDING SITE FOR RESIDUE ZN A 1502
2AC2SOFTWARECYS B:2046 , HIS B:2067 , CYS B:2173 , NAP B:3292 , GOL B:8002BINDING SITE FOR RESIDUE ZN B 1503
3AC3SOFTWARECYS B:2097 , CYS B:2100 , CYS B:2103 , CYS B:2111BINDING SITE FOR RESIDUE ZN B 2501
4AC4SOFTWARECYS A:1097 , CYS A:1100 , CYS A:1103 , CYS A:1111BINDING SITE FOR RESIDUE ZN A 2502
5AC5SOFTWAREHOH B:68 , HOH B:70 , HOH B:80 , HOH B:83 , HOH B:84 , HOH B:85 , HOH B:309 , ZN B:1503 , CYS B:2046 , GLY B:2047 , SER B:2048 , CYS B:2173 , THR B:2177 , GLY B:2198 , LEU B:2199 , GLY B:2200 , GLY B:2201 , VAL B:2202 , GLY B:2222 , THR B:2223 , HIS B:2224 , LYS B:2227 , CYS B:2267 , ALA B:2268 , ARG B:2270 , LEU B:2291 , SER B:2316 , VAL B:2317 , PHE B:2318 , ARG B:2367 , GOL B:8002BINDING SITE FOR RESIDUE NAP B 3292
6AC6SOFTWAREHOH A:107 , HOH A:110 , HOH A:186 , HOH A:187 , HOH A:209 , HOH A:261 , HOH A:307 , CYS A:1046 , GLY A:1047 , SER A:1048 , CYS A:1173 , THR A:1177 , GLY A:1198 , LEU A:1199 , GLY A:1200 , GLY A:1201 , VAL A:1202 , GLY A:1222 , THR A:1223 , HIS A:1224 , LYS A:1227 , CYS A:1267 , ALA A:1268 , GLY A:1269 , ARG A:1270 , LEU A:1291 , GLY A:1292 , LEU A:1293 , SER A:1316 , VAL A:1317 , PHE A:1318 , ARG A:1367 , ZN A:1502 , GOL A:8001BINDING SITE FOR RESIDUE NAP A 4292
7AC7SOFTWARESER A:1048 , HIS A:1067 , MET A:1116 , MET A:1141 , ZN A:1502 , NAP A:4292BINDING SITE FOR RESIDUE GOL A 8001
8AC8SOFTWAREZN B:1503 , SER B:2048 , HIS B:2067 , MET B:2116 , MET B:2141 , LEU B:2293 , NAP B:3292BINDING SITE FOR RESIDUE GOL B 8002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P0F)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:1061 -Pro A:1062
2Phe B:2061 -Pro B:2062

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P0F)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_ZINCPS00059 Zinc-containing alcohol dehydrogenases signature.ADH8_PELPE67-81
 		  2A:1066-1080
B:2066-2080

(-) Exons   (0, 0)

(no "Exon" information available for 1P0F)

(-) 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:372
 aligned with ADH8_PELPE | O57380 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:372
                                    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       371  
          ADH8_PELPE      2 CTAGKDITCKAAVAWEPHKPLSLETITVAPPKAHEVRIKILASGICGSDSSVLKEIIPSKFPVILGHEAVGVVESIGAGVTCVKPGDKVIPLFVPQCGSCRACKSSNSNFCEKNDMGAKTGLMADMTSRFTCRGKPIYNLVGTSTFTEYTVVADIAVAKIDPKAPLESCLIGCGFATGYGAAVNTAKVTPGSTCAVFGLGGVGFSAIVGCKAAGASRIIGVGTHKDKFPKAIELGATECLNPKDYDKPIYEVICEKTNGGVDYAVECAGRIETMMNALQSTYCGSGVTVVLGLASPNERLPLDPLLLLTGRSLKGSVFGGFKGEEVSRLVDDYMKKKINVNFLVSTKLTLDQINKAFELLSSGQGVRSIMIY  373
               SCOP domains d1p0fa1 A:1001-1163,A:1338-1372 Alcohol dehydrogenase                                                                                                              d1p0fa2 A:1164-1337 Alcohol dehydrogenase                                                                                                                                     d1p0fa1 A:1001-1163,A:1338-1372     SCOP domains
               CATH domains 1p0fA01 A:1001-1177,A:1317-1372 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                            1p0fA02 A:1178-1316 NAD(P)-binding Rossmann-like Domain                                                                                    1p0fA01 A:1001-1177,A:1317-1372                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee........eeeeeee......eeeeeeeeee.hhhhhhhhh..............eeeeeeee...........eeee........hhhhhh........................eee..eee...........eeeee...eeee....hhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeehhhhh..hhhhhhhhhh.....eeee...hhhhhhhhhhh......eeee.........eee.hhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...hhhh.eeeeehhhhhhhhhhhh......eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------ADH_ZINC       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1p0f A 1001 CTAGKDITCKAAVAWEPHKPLSLETITVAPPKAHEVRIKILASGICGSDSSVLKEIIPSKFPVILGHEAVGVVESIGAGVTCVKPGDKVIPLFVPQCGSCRACKSSNSNFCEKNDMGAKTGLMADMTSRFTCRGKPIYNLMGTSTFTEYTVVADIAVAKIDPKAPLESCLIGCGFATGYGAAVNTAKVTPGSTCAVFGLGGVGFSAIVGCKAAGASRIIGVGTHKDKFPKAIELGATECLNPKDYDKPIYEVICEKTNGGVDYAVECAGRIETMMNALQSTYCGSGVTVVLGLASPNERLPLDPLLLLTGRSLKGSVFGGFKGEEVSRLVDDYMKKKINVNFLVSTKLTLDQINKAFELLSSGQGVRSIMIY 1372
                                  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      1360      1370  


Chain B from PDB  Type:PROTEIN  Length:372
 aligned with ADH8_PELPE | O57380 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:372
                                    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       371  
          ADH8_PELPE      2 CTAGKDITCKAAVAWEPHKPLSLETITVAPPKAHEVRIKILASGICGSDSSVLKEIIPSKFPVILGHEAVGVVESIGAGVTCVKPGDKVIPLFVPQCGSCRACKSSNSNFCEKNDMGAKTGLMADMTSRFTCRGKPIYNLVGTSTFTEYTVVADIAVAKIDPKAPLESCLIGCGFATGYGAAVNTAKVTPGSTCAVFGLGGVGFSAIVGCKAAGASRIIGVGTHKDKFPKAIELGATECLNPKDYDKPIYEVICEKTNGGVDYAVECAGRIETMMNALQSTYCGSGVTVVLGLASPNERLPLDPLLLLTGRSLKGSVFGGFKGEEVSRLVDDYMKKKINVNFLVSTKLTLDQINKAFELLSSGQGVRSIMIY  373
               SCOP domains d1p0fb1 B:2001-2163,B:2338-2372 Alcohol dehydrogenase                                                                                                              d1p0fb2 B:2164-2337 Alcohol dehydrogenase                                                                                                                                     d1p0fb1 B:2001-2163,B:2338-2372     SCOP domains
               CATH domains 1p0fB01 B:2001-2177,B:2317-2372 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                            1p0fB02 B:2178-2316 NAD(P)-binding Rossmann-like Domain                                                                                    1p0fB01 B:2001-2177,B:2317-2372                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee........eeeeeee......eeeeeeeeee.hhhhhhhhh..............eeeeeeee...........eeee........hhhhhh........................eee..eee...........eeeee...eeee....hhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeehhhhh..hhhhhhhhhh.....eeee...hhhhhhhhhhh......eeee.........eee.hhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...hhhh.eeeeehhhhhhhhhhhh......eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------ADH_ZINC       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1p0f B 2001 CTAGKDITCKAAVAWEPHKPLSLETITVAPPKAHEVRIKILASGICGSDSSVLKEIIPSKFPVILGHEAVGVVESIGAGVTCVKPGDKVIPLFVPQCGSCRACKSSNSNFCEKNDMGAKTGLMADMTSRFTCRGKPIYNLMGTSTFTEYTVVADIAVAKIDPKAPLESCLIGCGFATGYGAAVNTAKVTPGSTCAVFGLGGVGFSAIVGCKAAGASRIIGVGTHKDKFPKAIELGATECLNPKDYDKPIYEVICEKTNGGVDYAVECAGRIETMMNALQSTYCGSGVTVVLGLASPNERLPLDPLLLLTGRSLKGSVFGGFKGEEVSRLVDDYMKKKINVNFLVSTKLTLDQINKAFELLSSGQGVRSIMIY 2372
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   Legend:   → Mismatch (orange background)
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    → 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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1P0F)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ADH8_PELPE | O57380)
molecular function
    GO:0008106    alcohol dehydrogenase (NADP+) activity    Catalysis of the reaction: an alcohol + NADP+ = an aldehyde + NADPH + H+.
    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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  1p0f
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  ADH8_PELPE | O57380
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  1.1.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        ADH8_PELPE | O57380: 1p0c

(-) Related Entries Specified in the PDB File

1p0c NATIVE NADP-DEPENDENT ALCOHOL DEHYDROGENASE