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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PKS11 REVEALS INTERMEDIATES IN THE SYNTHESIS OF METHYL-BRANCHED ALKYLPYRONES
 
Authors :  K. Gokulan, J. C. Sacchettini, Mycobacterium Tuberculosis Structu Proteomics Project (Xmtb)
Date :  22 Feb 13  (Deposition) - 24 Apr 13  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Lipid Biosynthesis, Structural Genomics, Enzyme Function Initiative, Ketosynthase Enzyme, Alkylpyrone Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Gokulan, S. E. O'Leary, W. K. Russell, D. H. Russell, M. Lalgondar, T. P. Begley, T. R. Ioerger, J. C. Sacchettini
Crystal Structure Of Mycobacterium Tuberculosis Polyketide Synthase 11 (Pks11) Reveals Intermediates In The Synthesis Of Methyl-Branched Alkylpyrones.
J. Biol. Chem. V. 288 16484 2013
PubMed-ID: 23615910  |  Reference-DOI: 10.1074/JBC.M113.468892

(-) Compounds

Molecule 1 - ALPHA-PYRONE SYNTHESIS POLYKETIDE SYNTHASE-LIKE PKS11
    Chains: A, C, B, D
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: MYCOBACTERIUM SMEGMATIS
    Expression System Taxid: 1772
    Expression System Vector Type: DEST17
    Gene: PKS11, RV1665, MT1705
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: ALPHA-PYRONE SYNTHESIS POLYKETIDE SYNTHASE TYPE III PKS11, CHALCONE SYNTHASE-LIKE PROTEIN, CHS-LIKE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2PLM4Ligand/IonPALMITIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2PLM2Ligand/IonPALMITIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2PLM2Ligand/IonPALMITIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:106 , SER A:138 , SER A:169 , THR A:171 , GLY A:184 , THR A:185 , PHE A:188 , GLY A:229 , TRP A:230 , LEU A:239 , SER A:312 , PRO A:341 , HOH A:504BINDING SITE FOR RESIDUE PLM A 400
2AC2SOFTWAREVAL C:106 , SER C:138 , CYS C:168 , THR C:171 , TRP C:230 , LEU C:239 , SER C:312BINDING SITE FOR RESIDUE PLM C 401
3AC3SOFTWAREALA C:44 , VAL C:179 , SER C:180 , VAL C:183 , MET C:228 , LEU C:241 , GLY C:279 , PRO C:281 , LYS C:282 , VAL C:283BINDING SITE FOR RESIDUE COA C 402
4AC4SOFTWAREVAL B:106 , GLY B:137 , SER B:138 , THR B:171 , VAL B:175 , THR B:185 , PHE B:188 , TRP B:230 , SER B:312 , PRO B:341BINDING SITE FOR RESIDUE PLM B 401
5AC5SOFTWAREARG B:40 , LEU B:41 , ALA B:44 , SER B:138 , VAL B:179 , SER B:180 , VAL B:183 , LEU B:241 , PRO B:243 , LEU B:245 , HIS B:277 , GLY B:279 , PRO B:281 , LYS B:282 , VAL B:283 , ASN B:310BINDING SITE FOR RESIDUE COA B 402
6AC6SOFTWAREVAL D:106 , SER D:138 , CYS D:168 , THR D:171 , THR D:185 , PHE D:188 , MET D:228 , TRP D:230 , SER D:312BINDING SITE FOR RESIDUE PLM D 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JD3)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Val A:111 -Pro A:112
2Gly A:342 -Phe A:343
3Val C:111 -Pro C:112
4Gly C:342 -Phe C:343
5Val B:111 -Pro B:112
6Gly B:342 -Phe B:343
7Val D:111 -Pro D:112
8Gly D:342 -Phe D:343

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JD3)

(-) Exons   (0, 0)

(no "Exon" information available for 4JD3)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jd3a1 A:2-211 automated matches                                                                                                                                                                                 d4jd3a2 A:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eeeehhhhhhhhh....hhhhhhhhhhhhhh....eeee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeee........hhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeee...hhhhhh....eeeeeeeee.......eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh...hhh.eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jd3 A   2 SVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGSVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    11        21        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  


Chain B from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jd3b1 B:2-211 automated matches                                                                                                                                                                                 d4jd3b2 B:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeehhhhhhhhh....hhhhhhhhhhhhhhh...eee...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.......hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeeehhhhhhhhh....eeeeeeeee.......eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh......eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jd3 B   2 SVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGSVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    11        21        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  


Chain C from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jd3c1 C:2-211 automated matches                                                                                                                                                                                 d4jd3c2 C:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eeeehhhhhhhhh....hhhhhhhhhhhhhhh...eeee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeeehhhhhhhhh....eeeeeeeee...hhh.eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jd3 C   2 SVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGSVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    11        21        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  


Chain D from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jd3d1 D:2-211 automated matches                                                                                                                                                                                 d4jd3d2 D:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeehhhhhhhhhh...hhhhhhhhhhhhhh....eee...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.......hhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeeehhhhhhhh.....eeeeeeeee.......eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jd3 D   2 SVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGSVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    11        21        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
   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, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Fold: Thiolase-like (231)
(-)
Superfamily: Thiolase-like (231)
(-)
Family: automated matches (108)
(-)
Protein domain: automated matches (108)
(-)
Mycobacterium tuberculosis [TaxId: 1773] (11)
1ad4jd3a1A:2-211
1bd4jd3a2A:212-353
1cd4jd3b1B:2-211
1dd4jd3b2B:212-353
1ed4jd3c1C:2-211
1fd4jd3c2C:212-353
1gd4jd3d1D:2-211
1hd4jd3d2D:212-353

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JD3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JD3)

(-) Gene Ontology  (12, 21)

Asymmetric Unit(hide GO term definitions)

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  4jd3
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  PKS11_MYCTO | P9WPF2
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  PKS11_MYCTU | P9WPF3
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 Related Entries

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

UniProtKB/Swiss-Prot
        PKS11_MYCTO | P9WPF2: 4jao 4jap 4jaq 4jar 4jat
        PKS11_MYCTU | P9WPF3: 4jao 4jap 4jaq 4jar 4jat

(-) Related Entries Specified in the PDB File

4jao 4jap 4jaq 4jar 4jat