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(-) Description

Title :  CRYSTAL STRUCTURE OF PAAK1 IN COMPLEX WITH ATP FROM BURKHOLDERIA CENOCEPACIA
 
Authors :  A. Law, M. J. Boulanger
Date :  13 Dec 10  (Deposition) - 04 May 11  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    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  (7, 48)

Asymmetric/Biological Unit (7, 48)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2BME5Ligand/IonBETA-MERCAPTOETHANOL
3GOL5Ligand/IonGLYCEROL
4MG6Ligand/IonMAGNESIUM ION
5MSE20Mod. Amino AcidSELENOMETHIONINE
6PG41Ligand/IonTETRAETHYLENE GLYCOL
7SCN9Ligand/IonTHIOCYANATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:168 , ALA B:92 , PRO B:100 , HOH B:745BINDING SITE FOR RESIDUE SCN B 1431
02AC2SOFTWAREARG A:228 , BME A:506 , HOH A:618BINDING SITE FOR RESIDUE SCN A 1432
03AC3SOFTWAREALA B:224 , ARG B:228 , BME B:511 , HOH B:642BINDING SITE FOR RESIDUE SCN B 1432
04AC4SOFTWAREARG A:302 , PG4 A:507BINDING SITE FOR RESIDUE SCN A 1444
05AC5SOFTWARELYS A:399 , ARG B:62 , HOH B:1057 , HOH B:672BINDING SITE FOR RESIDUE SCN B 1433
06AC6SOFTWAREHOH A:937BINDING SITE FOR RESIDUE SCN A 1433
07AC7SOFTWAREALA A:92 , PRO A:100 , HOH B:816 , LYS B:168BINDING SITE FOR RESIDUE SCN A 1434
08AC8SOFTWARELEU A:7 , HOH A:645 , HOH A:999BINDING SITE FOR RESIDUE SCN A 1435
09AC9SOFTWAREPHE A:161 , GLN A:165 , GLY B:139 , LEU B:140 , HOH B:958BINDING SITE FOR RESIDUE SCN A 1436
10BC1SOFTWARETYR A:136 , THR A:142 , ALA A:214 , ILE A:236 , GLY A:238 , LEU A:239 , GLY A:244 , PRO A:245 , ATP A:508BINDING SITE FOR RESIDUE GOL A 1437
11BC2SOFTWARELEU B:189 , HIS B:356 , ILE B:416 , GLU B:417 , SER B:419 , HOH B:662 , HOH B:790 , HOH B:730 , HOH B:875BINDING SITE FOR RESIDUE GOL B 1434
12BC3SOFTWARETYR B:136 , PHE B:141 , ALA B:214 , ILE B:236 , GLY B:238 , PRO B:245 , LYS B:422 , ATP B:512 , HOH B:904BINDING SITE FOR RESIDUE GOL B 1435
13BC4SOFTWAREHIS A:36 , PHE A:80 , ALA A:81 , VAL A:82 , ARG B:42 , GLU B:46 , HOH B:691BINDING SITE FOR RESIDUE GOL B 1436
14BC5SOFTWAREARG A:41 , HOH A:737 , HIS B:36 , PHE B:80 , VAL B:82 , HOH B:742 , HOH B:601 , HOH B:605BINDING SITE FOR RESIDUE GOL B 1437
15BC6SOFTWAREILE B:10 , ARG B:25 , ASP B:263 , HIS B:264 , ARG B:334 , HOH B:643BINDING SITE FOR RESIDUE BME B 1438
16BC7SOFTWAREPRO A:382 , THR B:313 , ARG B:315 , THR B:316 , HOH B:653BINDING SITE FOR RESIDUE BME B 1439
17BC8SOFTWAREGLY B:95 , GLY B:98 , LYS B:99 , PRO B:100BINDING SITE FOR RESIDUE BME B 1440
18BC9SOFTWAREARG A:228 , CYS A:377 , SCN A:501BINDING SITE FOR RESIDUE BME A 1438
19CC1SOFTWAREARG B:228 , CYS B:377 , PRO B:378 , SCN B:502BINDING SITE FOR RESIDUE BME B 1441
20CC2SOFTWAREALA A:47 , SER A:61 , ARG A:62 , PHE A:63 , PRO A:64 , PHE A:65 , GLU A:276 , SCN A:512 , HOH A:805BINDING SITE FOR RESIDUE PG4 A 1439
21CC3SOFTWARELYS A:68 , SER A:93 , SER A:94 , GLY A:95 , THR A:96 , THR A:97 , PHE A:141 , 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 , ASP A:305 , ILE A:323 , ARG A:326 , LYS A:422 , GOL A:505 , MG A:509 , HOH A:638 , HOH A:702 , HOH A:663 , HOH A:776 , HOH A:735 , HOH A:720 , HOH A:833 , HOH A:650BINDING SITE FOR RESIDUE ATP A 1440
22CC4SOFTWARELYS B:68 , SER B:93 , SER B:94 , GLY B:95 , THR B:96 , THR B:97 , PHE B:141 , 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 , ASP B:305 , ILE B:323 , ARG B:326 , LYS B:422 , GOL B:505 , MG B:514 , HOH B:644 , HOH B:713 , HOH B:620 , HOH B:666 , HOH B:738 , HOH B:876 , HOH B:752 , HOH B:777BINDING SITE FOR RESIDUE ATP B 1442
23CC5SOFTWAREATP A:508 , HOH A:638 , HOH A:702 , HOH A:735 , HOH A:720BINDING SITE FOR RESIDUE MG A 1441
24CC6SOFTWAREGLN B:350 , LEU B:353 , HOH B:654 , HOH B:869 , HOH B:871 , HOH B:642BINDING SITE FOR RESIDUE MG B 1443
25CC7SOFTWAREGLN A:350 , LEU A:353 , HOH A:848 , HOH A:713 , HOH A:635 , HOH A:618BINDING SITE FOR RESIDUE MG A 1442
26CC8SOFTWAREATP B:512 , HOH B:620 , HOH B:666 , HOH B:752 , HOH B:777BINDING SITE FOR RESIDUE MG B 1444
27CC9SOFTWAREVAL B:203 , SER B:205 , LEU B:207 , MSE B:229 , GLY B:230BINDING SITE FOR RESIDUE MG B 1445
28DC1SOFTWAREVAL A:203 , SER A:205 , LEU A:207 , MSE A:229 , GLY A:230 , HOH A:960BINDING SITE FOR RESIDUE MG A 1443

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y27)

(-) 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 2Y27)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y27)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y27)

(-) 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:425
 aligned with B4E7B5_BURCJ | B4E7B5 from UniProtKB/TrEMBL  Length:432

    Alignment length:425
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426     
         B4E7B5_BURCJ     7 LEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDKRK 431
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhh...hhhhhhhh........hhhhh.eeee.........eeeehhhhhhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh..hhhhh...eeeee....hhhhhhhhhhhhh.eeeeee..........ee.........ee....eeeeee.............eeeeeee..........eeeeeee.ee........ee....ee.hhheee..eeehhhhhhhhhh.........eeeeeee..eeeeeeee........hhhhhhhhhhhhhhhhhhhhh..eeeee...............eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y27 A   7 LEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLRDSYPFGmFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIImVTPSYmLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDmRVAIEQRmGIDAVDIYGLSEVmGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGTARTmRRmEKITGRSDDmmIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDKRK 431
                                    16        26        36        46        56        66        76  |     86        96       106       116       126       136       146       156       166       176     | 186 |     196       206       216    |  226  |    236      |246       256       266       276       286       296       306       316|  |   326   ||  336       346       356       366       376       386       396       406       416       426     
                                                                                                   79-MSE                                                                                                182-MSE |                              221-MSE 229-MSE       243-MSE                                                                   317-MSE      330-MSE                                                                                                 
                                                                                                                                                                                                               188-MSE                                                                                                                             320-MSE    331-MSE                                                                                                


Chain B from PDB  Type:PROTEIN  Length:427
 aligned with B4E7B5_BURCJ | B4E7B5 from UniProtKB/TrEMBL  Length:432

    Alignment length:427
                                    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 PLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDKR 430
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------AMP-binding-2y27B01 B:63-355                                                                                                                                                                                                                                                                         --------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------AMP-binding-2y27B02 B:63-355                                                                                                                                                                                                                                                                         --------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhh...hhhhhhhh........hhhhh.eeee.........eeeehhhhhhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh..hhhhh...eeeee....hhhhhhhhhhhhh.eeeeee..........ee.........ee....eeeeee.............eeeeeee..........eeeeeee.ee........ee....ee.hhheee..eeehhhhhhhhhh.........eeeeeee..eeeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhhh..eeeee...............eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y27 B   4 PLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLRDSYPFGmFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIImVTPSYmLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDmRVAIEQRmGIDAVDIYGLSEVmGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGTARTmRRmEKITGRSDDmmIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDKR 430
                                    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       
                                                                                                      79-MSE                                                                                                182-MSE |                              221-MSE 229-MSE       243-MSE                                                                   317-MSE      330-MSE                                                                                                
                                                                                                                                                                                                                  188-MSE                                                                                                                             320-MSE    331-MSE
   Legend:   → Mismatch (orange background)
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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 2Y27)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y27)

(-) 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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  2y27
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 Related Entries

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        B4E7B5_BURCJ | B4E7B5: 2y4n

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