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(-) Description

Title :  CRYSTAL STRUCTURE OF A C-C BOND HYDROLASE, BPHD, FROM BURKHOLDERIA XENOVORANS LB400
 
Authors :  S. Bhowmik, J. T. Bolin
Date :  08 May 07  (Deposition) - 22 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  C-C Bond Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. P. Horsman, S. Bhowmik, S. Y. Seah, P. Kumar, J. T. Bolin, L. D. Eltis
The Tautomeric Half-Reaction Of Bphd, A C-C Bond Hydrolase: Kinetic And Structural Evidence Supporting A Key Role For Histidine 265 Of The Catalytic Triad.
J. Biol. Chem. V. 282 19894 2007
PubMed-ID: 17442675  |  Reference-DOI: 10.1074/JBC.M702237200

(-) Compounds

Molecule 1 - 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE
    Chains: A, B
    EC Number: 3.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BPHD
    Organism Scientific: BURKHOLDERIA XENOVORANS
    Organism Taxid: 266265
    Strain: LB400

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MLI2Ligand/IonMALONATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MLI4Ligand/IonMALONATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:41 , GLY A:42 , GLY A:43 , ALA A:46 , ASN A:51 , ASN A:111 , SER A:112 , PHE A:175 , ARG A:190 , PHE A:239 , HIS A:265 , TRP A:266BINDING SITE FOR RESIDUE MLI A 287
2AC2SOFTWAREGLY B:41 , GLY B:42 , GLY B:43 , ALA B:46 , ASN B:51 , ASN B:111 , SER B:112 , ARG B:190 , PHE B:239 , HIS B:265 , TRP B:266BINDING SITE FOR RESIDUE MLI B 287

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PU5)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Met A:148 -Pro A:149
2Glu B:6 -Ser B:7
3Met B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PU5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PU5)

(-) Exons   (0, 0)

(no "Exon" information available for 2PU5)

(-) 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:285
 aligned with BPHD_PARXL | P47229 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:285
                                    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     
           BPHD_PARXL     2 TALTESSTSKFVKINEKGFSDFNIHYNEAGNGETVIMLHGGGPGAGGWSNYYRNVGPFVDAGYRVILKDSPGFNKSDAVVMDEQRGLVNARAVKGLMDALDIDRAHLVGNSMGGATALNFALEYPDRIGKLILMGPGGLGPSMFAPMPMEGIKLLFKLYAEPSYETLKQMLQVFLYDQSLITEELLQGRWEAIQRQPEHLKNFLISAQKAPLSTWDVTARLGEIKAKTFITWGRDDRFVPLDHGLKLLWNIDDARLHVFSKCGHWAQWEHADEFNRLVIDFLRHA 286
               SCOP domains d2pu5a_ A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (BPHD)                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeee.......eeeeeeee...eeeeee.......hhhhhhh.hhhhhhhh.eeeeee...............hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pu5 A   2 TALTESSTSKFVKINEKGFSDFNIHYNEAGNGETVIMLHGGGPGAGGWSNYYRNVGPFVDAGYRVILKDSPGFNKSDAVVMDEQRGLVNARAVKGLMDALDIDRAHLVGNSMGGATALNFALEYPDRIGKLILMGPGGLGPSMFAPMPMEGIKLLFKLYAEPSYETLKQMLQVFLYDQSLITEELLQGRWEAIQRQPEHLKNFLISAQKAPLSTWDVTARLGEIKAKTFITWGRDDRFVPLDHGLKLLWNIDDARLHVFSKCGHWAQWEHADEFNRLVIDFLRHA 286
                                    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     


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with BPHD_PARXL | P47229 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:283
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
           BPHD_PARXL     4 LTESSTSKFVKINEKGFSDFNIHYNEAGNGETVIMLHGGGPGAGGWSNYYRNVGPFVDAGYRVILKDSPGFNKSDAVVMDEQRGLVNARAVKGLMDALDIDRAHLVGNSMGGATALNFALEYPDRIGKLILMGPGGLGPSMFAPMPMEGIKLLFKLYAEPSYETLKQMLQVFLYDQSLITEELLQGRWEAIQRQPEHLKNFLISAQKAPLSTWDVTARLGEIKAKTFITWGRDDRFVPLDHGLKLLWNIDDARLHVFSKCGHWAQWEHADEFNRLVIDFLRHA 286
               SCOP domains d2pu5b_ B: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (BPHD)                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.......eeeeeeee....eeeee.......hhhhhhh.hhhhhhh...eeeee...............hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pu5 B   4 LTESSTSKFVKINEKGFSDFNIHYNEAGNGETVIMLHGGGPGAGGWSNYYRNVGPFVDAGYRVILKDSPGFNKSDAVVMDEQRGLVNARAVKGLMDALDIDRAHLVGNSMGGATALNFALEYPDRIGKLILMGPGGLGPSMFAPMPMEGIKLLFKLYAEPSYETLKQMLQVFLYDQSLITEELLQGRWEAIQRQPEHLKNFLISAQKAPLSTWDVTARLGEIKAKTFITWGRDDRFVPLDHGLKLLWNIDDARLHVFSKCGHWAQWEHADEFNRLVIDFLRHA 286
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PU5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PU5)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BPHD_PARXL | P47229)
molecular function
    GO:0018774    2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity    Catalysis of the reaction: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = benzoate + 2-oxopent-4-enoate.
    GO:0018771    2-hydroxy-6-oxonona-2,4-dienedioate hydrolase activity    Catalysis of the reaction: (2E,4Z)-2-hydroxy-6-oxonona-2,4-dienedioate + H2O = (2E)-2-hydroxypenta-2,4-dienoate + H+ + succinate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016823    hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances    Catalysis of the hydrolysis of any acid carbon-carbon bond in a ketonic substance, a substance containing a keto (C=O) group.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BPHD_PARXL | P47229: 2og1 2pu7 2puh 2puj 2rht 2rhw 2ri6 3v1k 3v1l 3v1m 3v1n

(-) Related Entries Specified in the PDB File

1c4x 1j1i 1u2e 2d0d 2pu6 2pu7 2puh 2puj