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(-) Description

Title :  CRYSTAL STRUCTURE OF PAAK2 IN COMPLEX WITH PHENYLACETYL ADENYLATE
 
Authors :  A. Law, M. J. Boulanger
Date :  07 Jan 11  (Deposition) - 09 Mar 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Phenylacetic Acid Degradation Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Law, M. J. Boulanger
Defining A Structural And Kinetic Rationale For Paralogous Copies Of Phenylacetate-Coa Ligases From The Cystic Fibrosis Pathogen Burkholderia Cenocepacia J2315.
J. Biol. Chem. V. 286 15577 2011
PubMed-ID: 21388965  |  Reference-DOI: 10.1074/JBC.M111.219683

(-) Compounds

Molecule 1 - PHENYLACETATE-COENZYME A LIGASE
    Chains: A, B
    EC Number: 6.2.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: BURKHOLDERIA CENOCEPACIA
    Organism Taxid: 216591
    Strain: J2315
    Synonym: PHENYLACETATE COA LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2DLL2Ligand/Ion5'-O-[HYDROXY(PHENYLACETYL)PHOSPHORYL]ADENOSINE
3K2Ligand/IonPOTASSIUM ION
4MG2Ligand/IonMAGNESIUM ION
5PEG5Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE B:140 , PHE B:145 , THR B:146 , GLY B:147 , ALA B:218 , GLU B:219 , PRO B:220 , ASP B:239 , ILE B:240 , TYR B:241 , GLY B:242 , LEU B:243 , SER B:244 , PRO B:249 , ASP B:309 , ARG B:330 , ILE B:336 , ASN B:341 , K B:1446 , HOH B:2329 , HOH B:2471 , HOH B:2472 , HOH B:2473BINDING SITE FOR RESIDUE DLL B1438
02AC2SOFTWAREARG A:157 , HOH A:2192 , HOH B:2474 , HOH B:2475BINDING SITE FOR RESIDUE PEG B1439
03AC3SOFTWAREARG A:45 , ASP A:49 , TYR B:38 , ARG B:45 , ASP B:49 , HOH B:2476BINDING SITE FOR RESIDUE PEG B1440
04AC4SOFTWAREALA B:65 , PHE B:67 , PRO B:68BINDING SITE FOR RESIDUE PEG B1441
05AC5SOFTWAREHIS B:43 , ARG B:46 , ASN B:78BINDING SITE FOR RESIDUE PEG B1442
06AC6SOFTWARETRP B:221 , THR B:222 , GLN B:223 , ARG B:226 , ASP B:239 , LYS B:326 , HOH B:2315 , HOH B:2330 , HOH B:2395BINDING SITE FOR RESIDUE PEG B1443
07AC7SOFTWAREGLN B:23 , GLN B:26 , GLU B:266 , ARG B:322 , HOH B:2083 , HOH B:2477BINDING SITE FOR RESIDUE BME B1444
08AC8SOFTWAREALA A:207 , SER A:209 , LEU A:211 , VAL A:233 , HOH A:2244 , HOH A:2264BINDING SITE FOR RESIDUE MG A1439
09AC9SOFTWAREALA B:207 , SER B:209 , LEU B:211 , VAL B:233 , HOH B:2303 , HOH B:2306BINDING SITE FOR RESIDUE MG B1445
10BC1SOFTWAREALA A:218 , GLY A:339 , ASN A:341 , DLL A:1441BINDING SITE FOR RESIDUE K A1440
11BC2SOFTWAREALA B:218 , GLY B:339 , ASN B:341 , DLL B:1438BINDING SITE FOR RESIDUE K B1446
12BC3SOFTWAREPHE A:140 , PHE A:145 , THR A:146 , GLY A:147 , ALA A:218 , GLU A:219 , PRO A:220 , ASP A:239 , ILE A:240 , TYR A:241 , GLY A:242 , LEU A:243 , SER A:244 , ASP A:309 , ARG A:330 , ILE A:336 , ASN A:341 , K A:1440 , HOH A:2139 , HOH A:2380 , HOH A:2381 , HOH A:2382 , HOH A:2383BINDING SITE FOR RESIDUE DLL A1441

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y4O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:79 -Pro A:80
2Tyr B:79 -Pro B:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y4O)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y4O)

(-) 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:433
 aligned with B4EL89_BURCJ | B4EL89 from UniProtKB/TrEMBL  Length:440

    Alignment length:433
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435   
         B4EL89_BURCJ     6 HPAAALEPIETASRDELQALQLERLKWSLRHAYDNVPHYRRTFDAAGVHPDDLKSLADLAKFPFSTKNDLRDNYPFGLFAVPREQVVRVHASSGTTGKPTVVGYTARDIDTWANVTARSIRAAGGRPGDTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDFEPKIILVTPSYMLNLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRVGIDALDIYGLSEVMGPGVACECVETKDGPVIWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLTKEAMPVIRYRTRDLTALLPPTARAMRRLAKITGRSDDMLIVRGVNVFPSQIEEIVVALPLLSGQFQITLSRDGHMDRLDLAVELRSEAAASVTDGERAALARELQHRIKTMVGVSSGVTVLAAGGIPATATGKARRVIDRRQ 438
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhh...hhhhhhh.........hhhhh.eeeee.......eeeeehhhhhhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh..hhhhh...eeeee....hhhhhhhhhhhhh.eeeeee..........eee.......eee....eeeeee.............eeeeeee..........eeeeeee.ee........ee....ee....eee..eeehhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeeeehhhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee...............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y4o A   6 HPAAALEPIETASRDELQALQLERLKWSLRHAYDNVPHYRRTFDAAGVHPDDLKSLADLAKFPFSTKNDLRDNYPFGLFAVPREQVVRVHASSGTTGKPTVVGYTARDIDTWANVTARSIRAAGGRPGDTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDFEPKIILVTPSYMLNLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRVGIDALDIYGLSEVMGPGVACECVETKDGPVIWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLTKEAMPVIRYRTRDLTALLPPTARAMRRLAKITGRSDDMLIVRGVNVFPSQIEEIVVALPLLSGQFQITLSRDGHMDRLDLAVELRSEAAASVTDGERAALARELQHRIKTMVGVSSGVTVLAAGGIPATATGKARRVIDRRQ 438
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435   


Chain B from PDB  Type:PROTEIN  Length:432
 aligned with B4EL89_BURCJ | B4EL89 from UniProtKB/TrEMBL  Length:440

    Alignment length:432
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435  
         B4EL89_BURCJ     6 HPAAALEPIETASRDELQALQLERLKWSLRHAYDNVPHYRRTFDAAGVHPDDLKSLADLAKFPFSTKNDLRDNYPFGLFAVPREQVVRVHASSGTTGKPTVVGYTARDIDTWANVTARSIRAAGGRPGDTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDFEPKIILVTPSYMLNLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRVGIDALDIYGLSEVMGPGVACECVETKDGPVIWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLTKEAMPVIRYRTRDLTALLPPTARAMRRLAKITGRSDDMLIVRGVNVFPSQIEEIVVALPLLSGQFQITLSRDGHMDRLDLAVELRSEAAASVTDGERAALARELQHRIKTMVGVSSGVTVLAAGGIPATATGKARRVIDRR 437
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------------------------------------------------AMP-binding-2y4oB01 B:76-359                                                                                                                                                                                                                                                                ------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------AMP-binding-2y4oB02 B:76-359                                                                                                                                                                                                                                                                ------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhh...hhhhhhhh........hhh.eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh..hhhhh...eeeee....hhhhhhhhhhhhh.eeeeee..........eee.......eee....eeeeee.............eeeeeee..........eeeeeee.ee........ee....ee....eee..eeehhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeeeehhhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee...............eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y4o B   6 HPAAALEPIETASRDELQALQLERLKWSLRHAYDNVPHYRRTFDAAGVHPDDLKSLADLAKFPFSTKNDLRDNYPFGLFAVPREQVVRVHASSGTTGKPTVVGYTARDIDTWANVTARSIRAAGGRPGDTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDFEPKIILVTPSYMLNLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRVGIDALDIYGLSEVMGPGVACECVETKDGPVIWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLTKEAMPVIRYRTRDLTALLPPTARAMRRLAKITGRSDDMLIVRGVNVFPSQIEEIVVALPLLSGQFQITLSRDGHMDRLDLAVELRSEAAASVTDGERAALARELQHRIKTMVGVSSGVTVLAAGGIPATATGKARRVIDRR 437
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 2Y4O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y4O)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: ANL (32)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B4EL89_BURCJ | B4EL89)
molecular function
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0047475    phenylacetate-CoA ligase activity    Catalysis of the reaction: ATP + CoA + phenylacetate = AMP + diphosphate + H(+) + phenylacetyl-CoA.
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.
    GO:0010124    phenylacetate catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylacetate.

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  6.2.1.30
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

2y4n PAAK1 IN COMPLEX WITH PHENYLACETYL ADENYLATE