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(-) Description

Title :  CRYSTAL STRUCTURE OF PHAB FROM RALSTONIA EUTROPHA
 
Authors :  K. Ikeda, Y. Tanaka, I. Tanaka, M. Yao
Date :  15 Oct 12  (Deposition) - 28 Aug 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha/Beta Structure, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Matsumoto, Y. Tanaka, T. Watanabe, R. Motohashi, K. Ikeda, K. Tobitani, M. Yao, I. Tanaka, S. Taguchi
Directed Evolution And Structural Analysis Of Nadph-Dependent Acetoacetyl Coenzyme A (Acetoacetyl-Coa) Reductase From Ralstonia Eutropha Reveals Two Mutations Responsible For Enhanced Kinetics
Appl. Environ. Microbiol. V. 79 6134 2013
PubMed-ID: 23913421  |  Reference-DOI: 10.1128/AEM.01768-13

(-) Compounds

Molecule 1 - ACETOACETYL-COA REDUCTASE
    ChainsA, B, C, D
    EC Number1.1.1.36
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePHBB, H16_A1439
    Organism CommonRALSTONIA EUTROPHA
    Organism ScientificCUPRIAVIDUS NECATOR
    Organism Taxid381666
    StrainATCC 17699 / H16 / DSM 428 / STANIER 337

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1DIO7Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL2Ligand/IonGLYCEROL
3SO47Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:13 , GLY A:14 , THR A:188 , ASP A:189 , MET A:190 , HOH A:421BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWARECYS A:34 , GLY A:35 , SER A:38 , ARG A:40BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREARG A:210 , HOH A:444 , HOH A:531 , HOH A:582 , GLY C:175BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWARETHR A:101 , ARG A:102 , ASN B:37 , HOH B:532 , TRP D:65BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWAREASN A:142 , GLN A:150 , TYR A:185 , HOH A:507BINDING SITE FOR RESIDUE DIO A 305
06AC6SOFTWAREGLY B:14 , THR B:188 , ASP B:189 , MET B:190 , HOH B:409BINDING SITE FOR RESIDUE SO4 B 301
07AC7SOFTWARECYS B:34 , GLY B:35 , SER B:38 , ARG B:40BINDING SITE FOR RESIDUE SO4 B 302
08AC8SOFTWAREASN A:61 , ALA A:63 , ASP A:64 , ASP A:110 , ASP B:64 , HOH B:542BINDING SITE FOR RESIDUE GOL B 303
09AC9SOFTWAREASN B:142 , GLN B:150 , MET B:190 , HOH B:421BINDING SITE FOR RESIDUE DIO B 304
10BC1SOFTWAREGLN B:3 , ARG B:4 , GLY B:27BINDING SITE FOR RESIDUE DIO B 305
11BC2SOFTWAREGLY C:13 , GLY C:14 , THR C:188 , ASP C:189 , MET C:190 , HOH C:548BINDING SITE FOR RESIDUE SO4 C 301
12BC3SOFTWAREASN C:142 , GLN C:150 , TYR C:185 , HOH C:445 , HOH C:467BINDING SITE FOR RESIDUE DIO C 302
13BC4SOFTWAREARG C:4 , GLY C:27 , PHE C:28BINDING SITE FOR RESIDUE DIO C 303
14BC5SOFTWAREGLY D:13 , GLY D:14 , THR D:188 , ASP D:189 , MET D:190BINDING SITE FOR RESIDUE SO4 D 301
15BC6SOFTWAREGLN D:3 , ARG D:4 , GLY D:27 , HOH D:529BINDING SITE FOR RESIDUE DIO D 302
16BC7SOFTWAREASN D:142 , GLN D:150 , HOH D:420 , HOH D:454BINDING SITE FOR RESIDUE DIO D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VZP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VZP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VZP)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.PHAB_CUPNH140-168
 
 
 
  4A:140-168
B:140-168
C:140-168
D:140-168

(-) Exons   (0, 0)

(no "Exon" information available for 3VZP)

(-) 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:245
 aligned with PHAB_CUPNH | P14697 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
           PHAB_CUPNH     2 TQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
               SCOP domains d3vzpa_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:140-168    ------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzp A   2 TQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with PHAB_CUPNH | P14697 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:249
                               1                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
           PHAB_CUPNH     - ---MTQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
               SCOP domains d3vzpb_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:140-168    ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzp B  -2 HHGSTQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         

Chain C from PDB  Type:PROTEIN  Length:244
 aligned with PHAB_CUPNH | P14697 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:244
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    
           PHAB_CUPNH     3 QRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
               SCOP domains d3vzpc_ C: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:140-168    ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzp C   3 QRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    

Chain D from PDB  Type:PROTEIN  Length:249
 aligned with PHAB_CUPNH | P14697 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:249
                               1                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
           PHAB_CUPNH     - ---MTQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
               SCOP domains d3vzpd_ D: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:140-168    ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzp D  -2 HHGSTQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VZP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VZP)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PHAB_CUPNH | P14697)
molecular function
    GO:0018454    acetoacetyl-CoA reductase activity    Catalysis of the reaction: (R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH + H+.
    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: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.
    GO:0042619    poly-hydroxybutyrate biosynthetic process    The chemical reactions and pathways resulting in the formation of poly-hydroxybutyrate (PHB), a polymer of beta-hydroxybutyrate and a common storage material of prokaryotic cells.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHAB_CUPNH | P146973vzq 3vzr 3vzs 4n5l 4n5m 4n5n

(-) Related Entries Specified in the PDB File

3vzq 3vzr 3vzs