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(-) Description

Title :  PAAK1 IN COMPLEX WITH PHENYLACETYL ADENYLATE
 
Authors :  A. Law, M. J. Boulanger
Date :  07 Jan 11  (Deposition) - 01 Mar 11  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
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 Fibrosi 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
    Fragment: RESIDUES 2-432
    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  (6, 12)

Asymmetric/Biological Unit (6, 12)
No.NameCountTypeFull Name
1BME3Ligand/IonBETA-MERCAPTOETHANOL
2DLL2Ligand/Ion5'-O-[HYDROXY(PHENYLACETYL)PHOSPHORYL]ADENOSINE
3MG4Ligand/IonMAGNESIUM ION
4PAC1Ligand/Ion2-PHENYLACETIC ACID
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
6PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:350 , LEU A:353 , HOH A:812 , HOH A:778 , HOH A:748 , HOH A:930BINDING SITE FOR RESIDUE MG A 1432
02AC2SOFTWAREVAL A:203 , SER A:205 , HOH A:964 , HOH A:616BINDING SITE FOR RESIDUE MG A 1433
03AC3SOFTWAREASN A:219 , ARG A:222 , LYS A:255 , ASP A:256 , GLY A:257 , LEU A:310 , GLU A:321 , LYS A:322 , HOH A:765 , HOH A:836BINDING SITE FOR RESIDUE PEG A 1434
04AC4SOFTWAREARG A:228 , ALA A:354 , CYS A:377 , HOH A:805BINDING SITE FOR RESIDUE BME A 1435
05AC5SOFTWARETYR A:136 , PHE A:141 , THR A:142 , GLY A:143 , ALA A:214 , GLU A:215 , PRO A:216 , ASP A:235 , ILE A:236 , TYR A:237 , GLY A:238 , LEU A:239 , SER A:240 , PRO A:245 , ASP A:305 , ARG A:326 , LYS A:422 , HOH A:877 , HOH A:605 , HOH A:651 , HOH A:632 , HOH A:714BINDING SITE FOR RESIDUE DLL A 1436
06AC6SOFTWAREGLN B:350 , ARG B:351 , LEU B:353 , HOH B:758 , HOH B:711 , HOH B:650 , HOH B:802BINDING SITE FOR RESIDUE MG B 1431
07AC7SOFTWAREVAL B:203 , SER B:205 , LEU B:207 , HOH B:846 , HOH B:644 , HOH B:731 , HOH B:715BINDING SITE FOR RESIDUE MG B 1432
08AC8SOFTWARESER B:94 , BME B:505 , HOH B:757 , HOH B:782 , HOH B:771BINDING SITE FOR RESIDUE PAC B 1433
09AC9SOFTWAREALA B:47 , SER B:61 , ARG B:62 , PHE B:63BINDING SITE FOR RESIDUE PGE B 1434
10BC1SOFTWAREHOH A:740 , ALA B:92 , GLY B:139 , LEU B:140 , PHE B:141 , PAC B:503 , HOH B:801BINDING SITE FOR RESIDUE BME B 1435
11BC2SOFTWAREGLU B:196 , ARG B:228 , ALA B:354 , CYS B:377 , HOH B:694BINDING SITE FOR RESIDUE BME B 1436
12BC3SOFTWARESER B:93 , PHE B:141 , THR B:142 , GLY B:143 , ALA B:214 , GLU B:215 , PRO B:216 , ASP B:235 , ILE B:236 , TYR B:237 , GLY B:238 , LEU B:239 , SER B:240 , PRO B:245 , ASP B:305 , ILE B:323 , ARG B:326 , LYS B:422 , HOH B:696 , HOH B:636 , HOH B:616BINDING SITE FOR RESIDUE DLL D 1437

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y4N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:75 -Pro A:76
2Tyr B:75 -Pro B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y4N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y4N)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y4N)

(-) 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:426
 aligned with B4E7B5_BURCJ | B4E7B5 from UniProtKB/TrEMBL  Length:432

    Alignment length:428
                                    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       293       303       313       323       333       343       353       363       373       383       393       403       413       423        
         B4E7B5_BURCJ     4 PLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDKRK 431
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhh...hhhhhhhh........hhhhh.eeee...--....eeeehhhhhhhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh..hhhhh...eeee.....hhhhhhhhhhhhh.eeeeee..........eee.......eee....eeeeee.............eeeeeee..........eeeeeee.ee........ee....ee....eee..eeehhhhhhhhhh.........eeeeeee..eeeeeeee........hhhhhhhhhhhhhhhhhhhhh..eeeee...............eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y4n A   4 PLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSG--GKPTVVGYTAADIDTWANLVARSIRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDKRK 431
                                    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       293       303       313       323       333       343       353       363       373       383       393       403       413       423        
                                                                                                                      95 98                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:423
 aligned with B4E7B5_BURCJ | B4E7B5 from UniProtKB/TrEMBL  Length:432

    Alignment length:426
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424      
         B4E7B5_BURCJ     5 LPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDKR 430
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------------------------------------AMP-binding-2y4nB01 B:63-355                                                                                                                                                                                                                                                                         --------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------AMP-binding-2y4nB02 B:63-355                                                                                                                                                                                                                                                                         --------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhh...hhhhhhhhh.......hhhhh.eeeee..---..eeeeehhhhhhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh..hhhhh...eeeee....hhhhhhhhhhhhh.eeeeee..........eee.......eee....eeeeee.............eeeeeee..........eeeeeee.ee........ee..........eee..eeehhhhhhhhhh....eeeeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhh..eeeee...............eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y4n B   5 LPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSG---KPTVVGYTAADIDTWANLVARSIRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDKR 430
                                    14        24        34        44        54        64        74        84        94|   |  104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424      
                                                                                                                     95  99
   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)
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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 2Y4N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y4N)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B4E7B5_BURCJ | B4E7B5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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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 Related Entries

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

UniProtKB/TrEMBL
        B4E7B5_BURCJ | B4E7B5: 2y27

(-) Related Entries Specified in the PDB File

2y27 CRYSTAL STRUCTURE OF PAAK1 IN COMPLEX WITH ATP FROM BURKHOLDERIA CENOCEPACIA
2y4o CRYSTAL STRUCTURE OF PAAK2 IN COMPLEX WITH PHENYLACETYL ADENYLATE