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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SECOND KETOSYNTHASE FROM THE BACILLAENE POLYKETIDE SYNTHASE BOUND TO A HEXANOYL SUBSTRATE MIMIC
 
Authors :  D. C. Gay, G. R. Gay, A. T. Keatinge-Clay
Date :  21 Oct 13  (Deposition) - 19 Feb 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Condensing Enzyme Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. C. Gay, G. Gay, A. J. Axelrod, M. Jenner, C. Kohlhaas, A. Kampa, N. J. Oldham, J. Piel, A. T. Keatinge-Clay
A Close Look At A Ketosynthase From A Trans-Acyltransferase Modular Polyketide Synthase.
Structure V. 22 444 2014
PubMed-ID: 24508341  |  Reference-DOI: 10.1016/J.STR.2013.12.016

(-) Compounds

Molecule 1 - POLYKETIDE SYNTHASE PKSJ
    Chains: A, B
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGAY28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Fragment: KETOSYNTHASE, UNP RESIDUES 3336-3953
    Gene: PKSJ, PKSK, BSU17180
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: PKS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
12JG2Mod. Amino Acid(2S)-2-AMINO-3-OXOPROPYL HEXANOATE
2SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:467 , MET A:507 , ASP A:508BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWAREARG A:495 , ARG A:597BINDING SITE FOR RESIDUE SO4 A 702
3AC3SOFTWAREARG B:495 , ARG B:597 , HOH B:803BINDING SITE FOR RESIDUE SO4 B 701
4AC4SOFTWAREASP B:42 , HIS B:610 , TRP B:612BINDING SITE FOR RESIDUE SO4 B 702
5AC5SOFTWARELYS B:467 , GLU B:505 , MET B:507 , ASP B:508BINDING SITE FOR RESIDUE SO4 B 703
6AC6SOFTWARESER B:13 , GLY B:14 , ASP B:21 , ILE B:22 , TYR B:99 , SER B:603BINDING SITE FOR RESIDUE SO4 B 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NA3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:531 -Lys A:532

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NA3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NA3)

(-) Exons   (0, 0)

(no "Exon" information available for 4NA3)

(-) 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:597
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhh....ee.........................ee................hhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhh....eeeee....hhhhhhhhh......hhhhhhh..hhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhh.......................eeeeeeeeehhhhhhhh....eeeeeeeeee..........hhhhhhhhhhhhhhhhh.hhh.eeeee.......hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhh.hhhhhhhhhhhhhhhhhhh.ee...................eee....ee...ee.....ee..eeeeeee....eeeeeeee.......eeeeeee.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhh.......eeee.hhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhh....................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4na3 A   3 DFEPVAIVGISGRFPGAMDIDEFWKNLEEGKDSITEVPKDRWDWREHYGNPDTDVNKTDIKWGGFIDGVAEFDPLFFGISPREADYVDPQQRLLMTYVWKALEDAGCSPQSLSGTGTGIFIGTGNTGYKDLFHRANLPIEGHAATGHMIPSVGPNRMSYFLNIHGPSEPVETAsSSSLVAIHRAVTAMQNGDCEMAIAGGVNTILTEEAHISYSKAGMLSTDGRCKTFSADANGYVRGEGVGMVMLKKLEDAERDGNHIYGVIRGTAENHGGRANTLTSPNPKAQADLLVRAYRQADIDPSTVTYIEAHGTGTELGDPIEINGLKAAFKELSNMDVPDHRCGIGSVKSNIGHLELAAGISGLIKVLLQMKHKTLVKSLHCETLNPYLQLTDSPFYIVQEKQEWKSVTDRDGNELPRRAGISSFGIGGVNAHIVIEEYMPEQPNVIVLSAKNKSRLIDRASQLLEVIRNKKYTDQDLHRIAYTLQVGREEMDERLACVAGTMQELEEKLQAFVDGKEETDEFFRGQSHRNKETQTIFTADEDMALALDAWIRKRKYAKLADLWVKGVSIQWNTLYGETKPRLISLPSYPFAKDHYWVP 614
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   |   182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332   ||  348       358       368       378       388       398       408       418       428       438       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       
                                                                                                                                                                                                       176-2JG                                                                                                                                                         336|                                                                                                     447|                                                                                                                                                             
                                                                                                                                                                                                                                                                                                                                                                        343                                                                                                      457                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:591
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhh.....ee......hhhhhh.............ee................hhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhh...eeeeee....hhhhhhhhh......hhhhhhh..hhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhh.......................eeeeeeeeehhhhhhhh....eeeeeeeeee..........hhhhhhhhhhhhhhhhh.hhhhh.eee.......hhhhhhhhhhhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhhhhhhhhhhh.ee...................eee....ee..............eeeeeee....eeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhh...eeee...hhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhh........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4na3 B   3 DFEPVAIVGISGRFPGAMDIDEFWKNLEEGKDSITEVPKDRWDWREHYGNPDTDVNKTDIKWGGFIDGVAEFDPLFFGISPREADYVDPQQRLLMTYVWKALEDAGCSPQSLSGTGTGIFIGTGNTGYKDLFHRANLPIEGHAATGHMIPSVGPNRMSYFLNIHGPSEPVETAsSSSLVAIHRAVTAMQNGDCEMAIAGGVNTILTEEAHISYSKAGMLSTDGRCKTFSADANGYVRGEGVGMVMLKKLEDAERDGNHIYGVIRGTAENHGGRANTLTSPNPKAQADLLVRAYRQADIDPSTVTYIEAHGTGTELGDPIEINGLKAAFKELSNMRDHRCGIGSVKSNIGHLELAAGISGLIKVLLQMKHKTLVKSLHCETLNPYLQLTDSPFYIVQEKQEWKSVTDRDGNELPRRAGISSFGIGGVNAHIVIEEYMPQPNVIVLSAKNKSRLIDRASQLLEVIRNKKYTDQDLHRIAYTLQVGREEMDERLACVAGTMQELEEKLQAFVDGKEFFRGQSHRNKETQTIFTADEDMALALDAWIRKRKYAKLADLWVKGVSIQWNTLYGETKPRLISLPSYPFAKDHYWVPA 615
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   |   182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    || 350       360       370       380       390       400       410       420       430       440      |460       470       480       490       500       510       520       530 ||    544       554       564       574       584       594       604       614 
                                                                                                                                                                                                       176-2JG                                                                                                                                                          337|                                                                                                  447|                                                                       532|                                                                              
                                                                                                                                                                                                                                                                                                                                                                         346                                                                                                   458                                                                        537
   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  (0, 0)

(no "SCOP Domain" information available for 4NA3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NA3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NA3)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:531 - Lys A:532   [ RasMol ]  
 

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  4na3
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  PKSJ_BACSU | P40806
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  2.3.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        PKSJ_BACSU | P40806: 4j1q 4j1s 4na1 4na2 5ktk

(-) Related Entries Specified in the PDB File

2hg4 PROTEIN HOMOLOG
2qo3 PROTEIN HOMOLOG
4na1
4na2