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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 :  19 Feb 13  (Deposition) - 24 Apr 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (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: D, C, B, A
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: MYCOBACTERIUM SMEGMATIS
    Expression System Taxid: 1772
    Gene: PKS11, RV1665, MT1705
    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):   CD
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
114U2Ligand/Ion(2S)-2-METHYL-3-OXOOCTADECANOIC ACID
2COA2Ligand/IonCOENZYME A
3PLM2Ligand/IonPALMITIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
114U-1Ligand/Ion(2S)-2-METHYL-3-OXOOCTADECANOIC ACID
2COA1Ligand/IonCOENZYME A
3PLM2Ligand/IonPALMITIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
114U2Ligand/Ion(2S)-2-METHYL-3-OXOOCTADECANOIC ACID
2COA1Ligand/IonCOENZYME A
3PLM-1Ligand/IonPALMITIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE D:25 , PHE D:28 , VAL D:106 , CYS D:138 , CYS D:168 , SER D:169 , THR D:171 , GLY D:184 , THR D:185 , PHE D:188 , TRP D:230 , SER D:312BINDING SITE FOR RESIDUE PLM D 401
2AC2SOFTWAREPHE C:25 , CYS C:138 , CYS C:168 , SER C:169 , THR C:171 , PHE C:188 , TRP C:230 , SER C:312BINDING SITE FOR RESIDUE PLM C 401
3AC3SOFTWAREALA C:44 , VAL C:179 , SER C:180 , VAL C:183 , LEU C:241 , GLY C:279 , GLY C:280 , PRO C:281 , LYS C:282 , MET C:339BINDING SITE FOR RESIDUE COA C 402
4AC4SOFTWARELEU B:56 , VAL B:106 , GLY B:137 , CYS B:138 , CYS B:168 , SER B:169 , THR B:171 , PHE B:188 , MET B:228 , TRP B:230 , SER B:312 , PRO B:341 , COA B:402BINDING SITE FOR RESIDUE 14U B 401
5AC5SOFTWARELEU B:41 , ALA B:44 , CYS B:138 , VAL B:179 , SER B:180 , VAL B:183 , LEU B:241 , HIS B:277 , GLY B:279 , PRO B:281 , LYS B:282 , ASN B:310 , 14U B:401BINDING SITE FOR RESIDUE COA B 402
6AC6SOFTWAREPHE A:25 , PHE A:28 , LEU A:52 , GLY A:137 , CYS A:138 , CYS A:168 , SER A:169 , THR A:171 , THR A:185 , PHE A:188 , MET A:228 , TRP A:230 , SER A:312 , PRO A:341BINDING SITE FOR RESIDUE 14U A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Val D:111 -Pro D:112
2Gly D:342 -Phe D: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 A:111 -Pro A:112
8Gly A:342 -Phe A:343

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JAP)

(-) 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:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4japa1 A:1-211 automated matches                                                                                                                                                                                  d4japa2 A:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....eeehhhhhhhhh....hhhhhhhhhhhhhh....eee...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.......hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeeeehhhhh.......eeeeeeeee...hhh.eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jap A   1 MSVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   


Chain B from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4japb1 B:2-211 automated matches                                                                                                                                                                                 d4japb2 B:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eeeehhhhhhhhh....hhhhhhhhhhhhhhh...eeee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.......hhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeee...hhhhhh....eeeeeeeee...hhh.eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jap B   2 SVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 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:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4japc1 C:1-211 automated matches                                                                                                                                                                                  d4japc2 C:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeehhhhhhhhh....hhhhhhhhhhhhhhh...eeee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.......hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeeehhhhhhhh.....eeeeeeeee.......eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jap C   1 MSVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   


Chain D from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4japd1 D:2-211 automated matches                                                                                                                                                                                 d4japd2 D:212-353 automated matches                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeehhhhhhhhh.......hhhhhhhhhhhh...eee......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.......hhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhh..hhhhhhhhhhh.eeeeeeeeehhhhhh.......eeeeeeeee...hhh.eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh...hhhheeeeee...hhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jap D   2 SVIAGVFGALPPHRYSQSEITDSFVEFPGLKEHEEIIRRLHAAAKVNGRHLVLPLQQYPSLTDFGDANEIFIEKAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPDDVAVLVSVELCSLTYPAVKPTVSSLVGTALFGDGAAAVVAVGDRRAEQVRAGGPDILDSRSSLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEALELTWRSLGEIGNLSSASILHILRDTIEKRPPSGSAGLMLAMGPGFCTELVLLRWR 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)
1ad4japa1A:1-211
1bd4japa2A:212-353
1cd4japb1B:2-211
1dd4japb2B:212-353
1ed4japc1C:1-211
1fd4japc2C:212-353
1gd4japd1D:2-211
1hd4japd2D:212-353

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 21)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PKS11_MYCTO | P9WPF2: 4jao 4jaq 4jar 4jat 4jd3
        PKS11_MYCTU | P9WPF3: 4jao 4jaq 4jar 4jat 4jd3

(-) Related Entries Specified in the PDB File

4jao 4jaq 4jar 4jat 4jd3