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(-) Description

Title :  SUBSTRATE-DIRECTED DUAL CATALYSIS OF DICARBONYL COMPOUNDS BY DIKETOREDUCTASE
 
Authors :  M. Lu, M. A. White, Y. Huang, X. Wu, N. Liu, X. Cheng, Y. Chen
Date :  05 Mar 12  (Deposition) - 14 Nov 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Nadh (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lu, Y. Huang, M. A. White, X. Wu, N. Liu, X. Cheng, Y. Chen
Dual Catalysis Mode For The Dicarbonyl Reduction Catalyzed By Diketoreductase
Chem. Commun. (Camb. ) V. 48 11352 2012
PubMed-ID: 23073461  |  Reference-DOI: 10.1039/C2CC36334H

(-) Compounds

Molecule 1 - DIKETOREDUCTASE
    Chains: A
    Organism Scientific: ACINETOBACTER BAYLYI
    Organism Taxid: 202950
    Other Details: PURCHASED FROM INVITROGEN BIO INC

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2GOL4Ligand/IonGLYCEROL
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2GOL8Ligand/IonGLYCEROL
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , THR A:12 , GLY A:13 , VAL A:14 , LEU A:15 , ASP A:34 , ILE A:35 , VAL A:93 , PRO A:94 , GLU A:95 , LEU A:99 , LYS A:100 , ASN A:120 , SER A:121 , SER A:122 , HIS A:143 , PHE A:144 , ARG A:256 , GOL A:302 , 1PE A:306BINDING SITE FOR RESIDUE NAD A 301
2AC2SOFTWARETHR A:12 , ASP A:34 , ALA A:39 , ALA A:42 , ARG A:46 , PRO A:253 , ARG A:256 , NAD A:301BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWAREGLY A:225BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWAREGLU A:234 , TYR A:281 , ARG A:282BINDING SITE FOR RESIDUE GOL A 304
5AC5SOFTWAREARG A:74 , GLN A:81 , ALA A:82 , VAL A:83 , LYS A:84 , ASP A:85 , ALA A:86BINDING SITE FOR RESIDUE GOL A 305
6AC6SOFTWARESER A:122 , LEU A:201 , ASP A:202 , VAL A:239 , SER A:248 , NAD A:301BINDING SITE FOR RESIDUE 1PE A 306
7AC7SOFTWAREGLY A:240 , LEU A:241 , THR A:242 , THR A:243 , LYS A:263 , LEU A:272 , HOH A:426BINDING SITE FOR RESIDUE SO4 A 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E13)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E13)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E13)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E13)

(-) Exons   (0, 0)

(no "Exon" information available for 4E13)

(-) 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 A from PDB  Type:PROTEIN  Length:283
 aligned with B1P3E1_ACIBI | B1P3E1 from UniProtKB/TrEMBL  Length:283

    Alignment length:283
                                    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   
         B1P3E1_ACIBI     1 MTGITNVTVLGTGVLGSQIAFQTAFHGFAVTAYDINTDALDAAKKRFEGLAAVYEKEVAGAADGAAQKALGGIRYSDDLAQAVKDADLVIEAVPESLDLKRDIYTKLGELAPAKTIFATNSSTLLPSDLVGYTGRGDKFLALHFANHVWVNNTAEVMGTTKTDPEVYQQVVEFASAIGMVPIELKKEKAGYVLNSLLVPLLDAAAELLVDGIADPETIDKTWRIGTGAPKGPFEIFDIVGLTTAYNISSVSGPKQREFAAYLKENYIDKGKLGLATGEGFYRY 283
               SCOP domains d4e13a1 A:1-189 automated matches                                                                                                                                                            d4e13a2 A:190-283 automated matches                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.eee.hhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhh.eeeeee........eeeeee....hhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e13 A   1 MTGITNVTVLGTGVLGSQIAFQTAFHGFAVTAYDINTDALDAAKKRFEGLAAVYEKEVAGAADGAAQKALGGIRYSDDLAQAVKDADLVIEAVPESLDLKRDIYTKLGELAPAKTIFATNSSTLLPSDLVGYTGRGDKFLALHFANHVWVNNTAEVMGTTKTDPEVYQQVVEFASAIGMVPIELKKEKAGYVLNSLLVPLLDAAAELLVDGIADPETIDKTWRIGTGAPKGPFEIFDIVGLTTAYNISSVSGPKQREFAAYLKENYIDKGKLGLATGEGFYRY 283
                                    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
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E13)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E13)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (B1P3E1_ACIBI | B1P3E1)
molecular function
    GO:0003857    3-hydroxyacyl-CoA dehydrogenase activity    Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H(+).
    GO:0070403    NAD+ binding    Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    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:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    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/TrEMBL
        B1P3E1_ACIBI | B1P3E1: 4dyd 4e12

(-) Related Entries Specified in the PDB File

4dyd 4e12