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(-) Description

Title :  CRYSTAL STRUCTURE OF MAMMALIAN DIMERIC DIHYDRODIOL DEHYDROGENASE
 
Authors :  V. Carbone, O. El-Kabbani
Date :  04 Dec 06  (Deposition) - 31 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (2x)
Keywords :  Nadp-Binding Rossmann-Fold Domain, Predominantly Anti-Parallel Beta Sheet, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Carbone, S. Endo, R. Sumii, R. P. Chung, T. Matsunaga, A. Hara, O. El-Kabbani
Structures Of Dimeric Dihydrodiol Dehydrogenase Apoenzyme And Inhibitor Complex: Probing The Subunit Interface With Site-Directed Mutagenesis.
Proteins V. 70 176 2008
PubMed-ID: 17654552  |  Reference-DOI: 10.1002/PROT.21566

(-) Compounds

Molecule 1 - DIMERIC DIHYDRODIOL DEHYDROGENASE
    Chains: X
    EC Number: 1.3.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PKK223-3
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Common: CRAB-EATING MACAQUE
    Organism Scientific: MACACA FASCICULARIS
    Organism Taxid: 9541

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (2x): X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1AC61Ligand/IonP-HYDROXYACETOPHENONE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1AC62Ligand/IonP-HYDROXYACETOPHENONE
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3SO48Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH X:26 , ARG X:1114 , VAL X:1309 , GLU X:1312BINDING SITE FOR RESIDUE SO4 X 1335
2AC2SOFTWARESER X:1009 , VAL X:1010 , ALA X:1036 , ARG X:1037 , ARG X:1041 , TYR X:1058BINDING SITE FOR RESIDUE SO4 X 1336
3AC3SOFTWAREHOH X:158 , LEU X:1012 , GLN X:1075 , ARG X:1163BINDING SITE FOR RESIDUE SO4 X 1337
4AC4SOFTWAREHOH X:175 , ALA X:1002 , LEU X:1003 , ARG X:1293 , ARG X:1297BINDING SITE FOR RESIDUE SO4 X 1338
5AC5SOFTWAREHOH X:131 , HOH X:196 , LEU X:1177 , TRP X:1254 , ASP X:1280BINDING SITE FOR RESIDUE AC6 X 2001
6AC6SOFTWARETYR X:1180 , GLN X:1183 , PHE X:1184 , CYS X:1253 , TRP X:1254BINDING SITE FOR RESIDUE BME X 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O48)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys X:1097 -Pro X:1098
2Asn X:1251 -Pro X:1252
3Val X:1273 -Pro X:1274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O48)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O48)

(-) Exons   (0, 0)

(no "Exon" information available for 2O48)

(-) Sequences/Alignments

Asymmetric 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 X from PDB  Type:PROTEIN  Length:331
 aligned with DHDH_MACFA | Q9TQS6 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:331
                                    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 
          DHDH_MACFA      2 ALRWGIVSVGLISSDFTAVLQTLPRSEHQVVAVAARDLSRAKEFAQKHDIPKAYGSYEELAKDPNVEVAYVGTQHPQHKAAVMLCLAAGKAVLCEKPMGVNAAEVREMVTEARSRGLFLMEAIWTRFFPASEALRSVLAQGTLGDLRVARAEFGKNLTHVPRAVDWAQAGGALLDLGIYCVQFISMVFGGQKPEKISVMGRRHETGVDDTVTVLLQYPGEVHGSFTCSITAQLSNTASVSGTKGMAQLLNPCWCPTELVVKGEHKEFLLPPVPKNCNFDNGAGMSYEAKHVRECLRKGLKESPVIPLVESELLADILEEVRRAIGVTFPQD  332
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -GFO_IDH_MocA-2o48X01 X:1003-1124                                                                                          -----------GFO_IDH_MocA_C-2o48X02 X:1136-1243                                                                          ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhhh...ee.hhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeeeeeee.....eeeeeeeeee...eeeeeeee........eeeee..eeeee........eeee..eeee.............hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2o48 X 1002 ALRWGIVSVGLISSDFTAVLQTLPRSEHQVVAVAARDLSRAKEFAQKHDIPKAYGSYEELAKDPNVEVAYVGTQHPQHKAAVMLCLAAGKAVLCEKPMGVNAAEVREMVTEARSRGLFLMEAIWTRFFPASEALRSVLAQGTLGDLRVARAEFGKNLTHVPRAVDWAQAGGALLDLGIYCVQFISMVFGGQKPEKISVMGRRHETGVDDTVTVLLQYPGEVHGSFTCSITAQLSNTASVSGTKGMAQLLNPCWCPTELVVKGEHKEFLLPPVPKNCNFDNGAGMSYEAKHVRECLRKGLKESPVIPLVESELLADILEEVRRAIGVTFPQD 1332
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 2O48)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O48)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: ox_reductase_C (19)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain X   (DHDH_MACFA | Q9TQS6)
molecular function
    GO:0047837    D-xylose 1-dehydrogenase (NADP+) activity    Catalysis of the reaction: D-xylose + NADP(+) = D-xylono-1,5-lactone + H(+) + NADPH.
    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:0047115    trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity    Catalysis of the reaction: NADP+ + trans-1,2-dihydrobenzene-1,2-diol = NADPH + catechol.
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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  2o48
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  DHDH_MACFA | Q9TQS6
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  1.3.1.20
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 Related Entries

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

UniProtKB/Swiss-Prot
        DHDH_MACFA | Q9TQS6: 2o4u 2poq 3ohs

(-) Related Entries Specified in the PDB File

1ofg PROTEIN WITH SIMILAR SECONDARY STRUCTURE
2glx PROTEIN WITH SIMILAR SECONDARY STRUCTURE