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(-) Description

Title :  CRYSTAL STRUCTURE OF D-3-HYDROXYBUTYRATE DEHYDROGENASE FROM ALCALIGENES FAECALIS COMPLEXED WITH NAD+ AND AN INHIBITOR METHYLMALONATE
 
Authors :  H. Kanazawa, M. Tsunoda, M. M. Hoque, K. Suzuki, T. Yamamoto, A. Takenak
Date :  19 Apr 16  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Short-Chain Dehydrogenases/Reductases, Inhibitor, Complex, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kanazawa, M. M. Hoque, M. Tsunoda, K. Suzuki, T. Yamamoto, G. Kawai, J. Kondo, A. Takenaka
Structural Insights Into The Catalytic Reaction Trigger And Inhibition Of D-3-Hydroxybutyrate Dehydrogenase
Acta Crystallogr. , Sect. F V. 72 507 2016
PubMed-ID: 27380367  |  Reference-DOI: 10.1107/S2053230X16007767

(-) Compounds

Molecule 1 - 3-HYDROXYBUTYRATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UZ73_03715
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
    Synonym: D-3-HYDROXYBUTYRATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DXX1Ligand/IonMETHYLMALONIC ACID
3NA3Ligand/IonSODIUM ION
4NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DXX4Ligand/IonMETHYLMALONIC ACID
3NA-1Ligand/IonSODIUM ION
4NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , THR A:13 , SER A:14 , GLY A:15 , ILE A:16 , ASN A:34 , PHE A:36 , ALA A:62 , ASP A:63 , LEU A:64 , ASN A:90 , GLY A:92 , LEU A:113 , ILE A:140 , ALA A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , TRP A:187 , VAL A:188 , THR A:190 , PRO A:191 , LEU A:192 , VAL A:193 , DXX A:302 , HOH A:420 , HOH A:451 , HOH A:476 , HOH A:520 , HOH A:546 , HOH A:561binding site for residue NAD A 301
2AC2SOFTWAREGLN A:94 , SER A:142 , HIS A:144 , LYS A:152 , TYR A:155 , TRP A:187 , GLN A:196 , TRP A:257 , NAD A:301binding site for residue DXX A 302
3AC3SOFTWARESER A:149 , VAL A:150 , LYS A:219binding site for residue CL A 303
4AC4SOFTWAREVAL A:147 , ARG A:260 , HOH A:424 , HOH A:432binding site for residue NA A 304
5AC5SOFTWARELEU A:64 , SER A:65 , ALA A:112 , SER A:116 , ALA A:117 , HOH A:457 , HOH A:593binding site for residue NA A 305
6AC6SOFTWAREGLY A:4 , LYS A:6 , ASP A:85binding site for residue NA A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B4V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B4V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B4V)

(-) Exons   (0, 0)

(no "Exon" information available for 5B4V)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b4v A   1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
                                    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
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  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 5B4V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B4V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B4V)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        D0VWQ0_ALCFA | D0VWQ0: 2yz7 3vdq 3vdr 3w8d 3w8e 3w8f 5b4t 5b4u

(-) Related Entries Specified in the PDB File

5b4t 5b4u