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(-) Description

Title :  CRYSTAL STRUCTURES OF A BENZOATE COA LIGASE FROM BURKHOLDERIA XENOVORANS LB400
 
Authors :  M. J Boulanger, J. Bains
Date :  27 Jul 07  (Deposition) - 02 Oct 07  (Release) - 19 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase, Benzoate Oxidation, Benzoate Coa Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Bains, M. J. Boulanger
Biochemical And Structural Characterization Of The Paralogous Benzoate Coa Ligases From Burkholderia Xenovorans Lb400: Defining The Entry Point Into The Novel Benzoate Oxidation (Box) Pathway.
J. Mol. Biol. V. 373 965 2007
PubMed-ID: 17884091  |  Reference-DOI: 10.1016/J.JMB.2007.08.008

(-) Compounds

Molecule 1 - BENZOATE-COENZYME A LIGASE
    Chains: A, B
    EC Number: 6.2.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 1-529
    Organism Scientific: BURKHOLDERIA XENOVORANS
    Organism Taxid: 266265
    Other Details: BENZOATE
    Strain: LB400
    Synonym: BENZOATE COA LIGASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BEZ2Ligand/IonBENZOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BEZ1Ligand/IonBENZOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BEZ1Ligand/IonBENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:236 , TYR A:238 , ALA A:308 , GLY A:309 , GLY A:333 , SER A:334 , HIS A:339 , LYS A:520 , HOH A:2546 , HOH A:2547BINDING SITE FOR RESIDUE BEZ A1529
2AC2SOFTWAREPHE B:236 , TYR B:238 , ALA B:308 , GLY B:309 , GLY B:333 , SER B:334 , HIS B:339 , LYS B:520 , HOH B:2311 , HOH B:2515BINDING SITE FOR RESIDUE BEZ B1529

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V7B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:465 -Gly A:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V7B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V7B)

(-) Exons   (0, 0)

(no "Exon" information available for 2V7B)

(-) 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:489
 aligned with Q13WK3_PARXL | Q13WK3 from UniProtKB/TrEMBL  Length:530

    Alignment length:507
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
         Q13WK3_PARXL    22 LFNFAAYLFRLNETRAGKTAYIDDTGSTTYGELEERARRFASALRTLGVHPEERILLVMLDTVALPVAFLGALYAGVVPVVANTLLTPADYVYMLTHSHARAVIASGALVQNVTQALESAEHDGCQLIVSQPRESEPRLAPLFEELIDAAAPAAKAAATGCDDIAFWLYSSGSTGKPKGTVHTHANLYWTAELYAKPILGIAENDVVFSAAKLFFAYGLGNGLTFPLSVGATAILMAERPTADAIFARLVEHRPTVFYGVPTLYANMLVSPNLPARADVAIRICTSAGEALPREIGERFTAHFGCEILDGIGSTEMLHIFLSNRAGAVEYGTTGRPVPGYEIELRDEAGHAVPDGEVGDLYIKGPSAAVMYWNNREKSRATFLGEWIRSGDKYCRLPNGCYVYAGRSDDMLKVSGQYVSPVEVEMVLVQHDAVLEAAVVGVDHGGLVKTRAFVVLKREFAPSEILAEELKAFVKDRLAPHKYPRDIVFVDDLPKTATGKIQRFKLRE 528
               SCOP domains d2v7ba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..eeee....eeehhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh.---..eeeee..------...hhhhhhhh..............eeeeeee-----..eeeeeehhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhh.eee......hhhhhhhhhhhh...eeeehhhhhhhhhh.....hhhhh...eeee.....hhhhhhhhhhhhh..eeeeee......eeee............ee....eeeee............eeeeee..........hhhhhhhhee..eeeeeeeeee.....eeeeee.hhh..----..hhhhhhhhhh....eeeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhh.........eeeee...........hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v7b A  22 LFNFAAYLFRLNETRAGKTAYIDDTGSTTYGELEERARRFASALRTLGVHPEERILLVMLDTVALPVAFLGALYAGVVPVVANTLLTPADYVYMLTHSHARAVIASGALVQNVTQALESA---GCQLIVSQP------LAPLFEELIDAAAPAAKAAATGCDDIAFWLYS-----KPKGTVHTHANLYWTAELYAKPILGIAENDVVFSAAKLFFAYGLGNGLTFPLSVGATAILMAERPTADAIFARLVEHRPTVFYGVPTLYANMLVSPNLPARADVAIRICTSAGEALPREIGERFTAHFGCEILDGIGSTEMLHIFLSNRAGAVEYGTTGRPVPGYEIELRDEAGHAVPDGEVGDLYIKGPSAAVMYWNNREKSRATFLGEWIRSGDKYCRLPNGCYVYAGRSDDMLK----YVSPVEVEMVLVQHDAVLEAAVVGVDHGGLVKTRAFVVLKREFAPSEILAEELKAFVKDRLAPHKYPRDIVFVDDLPKTATGKIQRFKLRE 528
                                    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       341       351       361       371       381       391       401       411       421       431 |    |441       451       461       471       481       491       501       511       521       
                                                                                                                                                 141 145     153    160                            191   197                                                                                                                                                                                                                                         433  438                                                                                          


Chain B from PDB  Type:PROTEIN  Length:489
 aligned with Q13WK3_PARXL | Q13WK3 from UniProtKB/TrEMBL  Length:530

    Alignment length:507
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
         Q13WK3_PARXL    22 LFNFAAYLFRLNETRAGKTAYIDDTGSTTYGELEERARRFASALRTLGVHPEERILLVMLDTVALPVAFLGALYAGVVPVVANTLLTPADYVYMLTHSHARAVIASGALVQNVTQALESAEHDGCQLIVSQPRESEPRLAPLFEELIDAAAPAAKAAATGCDDIAFWLYSSGSTGKPKGTVHTHANLYWTAELYAKPILGIAENDVVFSAAKLFFAYGLGNGLTFPLSVGATAILMAERPTADAIFARLVEHRPTVFYGVPTLYANMLVSPNLPARADVAIRICTSAGEALPREIGERFTAHFGCEILDGIGSTEMLHIFLSNRAGAVEYGTTGRPVPGYEIELRDEAGHAVPDGEVGDLYIKGPSAAVMYWNNREKSRATFLGEWIRSGDKYCRLPNGCYVYAGRSDDMLKVSGQYVSPVEVEMVLVQHDAVLEAAVVGVDHGGLVKTRAFVVLKREFAPSEILAEELKAFVKDRLAPHKYPRDIVFVDDLPKTATGKIQRFKLRE 528
               SCOP domains d2v7bb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..eeee....eeehhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh.---..eeeee..------...hhhhhhhhh.............eeeeeee-----..eeeeeehhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhh.eee......hhhhhhhhhhhh...eeeehhhhhhhhhh.....hhhhh...eeee.....hhhhhhhhhhhhh.eeeeeee......eeee............ee....eeeee............eeeeee..........hhhhhhhhee..eeeeeeeeee.....eeeeee.hhh..----..hhhhhhhhhh....eeeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhh.........eeeee...........hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v7b B  22 LFNFAAYLFRLNETRAGKTAYIDDTGSTTYGELEERARRFASALRTLGVHPEERILLVMLDTVALPVAFLGALYAGVVPVVANTLLTPADYVYMLTHSHARAVIASGALVQNVTQALESA---GCQLIVSQP------LAPLFEELIDAAAPAAKAAATGCDDIAFWLYS-----KPKGTVHTHANLYWTAELYAKPILGIAENDVVFSAAKLFFAYGLGNGLTFPLSVGATAILMAERPTADAIFARLVEHRPTVFYGVPTLYANMLVSPNLPARADVAIRICTSAGEALPREIGERFTAHFGCEILDGIGSTEMLHIFLSNRAGAVEYGTTGRPVPGYEIELRDEAGHAVPDGEVGDLYIKGPSAAVMYWNNREKSRATFLGEWIRSGDKYCRLPNGCYVYAGRSDDMLK----YVSPVEVEMVLVQHDAVLEAAVVGVDHGGLVKTRAFVVLKREFAPSEILAEELKAFVKDRLAPHKYPRDIVFVDDLPKTATGKIQRFKLRE 528
                                    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       341       351       361       371       381       391       401       411       421       431 |    |441       451       461       471       481       491       501       511       521       
                                                                                                                                                 141 145     153    160                            191   197                                                                                                                                                                                                                                         433  438
   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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V7B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V7B)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q13WK3_PARXL | Q13WK3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016405    CoA-ligase activity    Catalysis of the reaction: substrate + ATP + CoASH = AMP + diphosphate + substrate-CoA.
    GO:0018858    benzoate-CoA ligase activity    Catalysis of the reaction: ATP + benzoate + CoA = AMP + benzoyl-CoA + diphosphate + H(+).
    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:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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        Q13WK3_PARXL | Q13WK3: 4gxq 4gxr

(-) Related Entries Specified in the PDB File

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