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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH TLM5
 
Authors :  J. Schiebel, K. Kapilashrami, A. Fekete, G. R. Bommineni, C. M. Schaefe M. J. Mueller, P. J. Tonge, C. Kisker
Date :  19 Sep 13  (Deposition) - 09 Oct 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Beto-Ketoacyl-Acp Synthase, Kas Enzyme, Condensing Enzyme, Type 2 Fatty Acid Biosynthesis, Mycolic Acid Synthesis, Thiolactomycin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Schiebel, K. Kapilashrami, A. Fekete, G. R. Bommineni, C. M. Schaefer, M. J. Mueller, P. J. Tonge, C. Kisker
Structural Basis For The Recognition Of Mycolic Acid Precursors By Kasa, A Condensing Enzyme And Drug Target From Mycobacterium Tuberculosis
J. Biol. Chem. V. 288 34190 2013
PubMed-ID: 24108128  |  Reference-DOI: 10.1074/JBC.M113.511436

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
    Chains: A, B
    EC Number: 2.3.1.41
    Engineered: YES
    Expression System: MYCOBACTERIUM SMEGMATIS
    Expression System Plasmid: PFPCA1
    Expression System Strain: MC2155
    Expression System Taxid: 1772
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS H37RV
    Organism Taxid: 83332
    Synonym: BETA-KETOACYL ACP SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 24)

Asymmetric/Biological Unit (4, 24)
No.NameCountTypeFull Name
1EDO18Ligand/Ion1,2-ETHANEDIOL
2K2Ligand/IonPOTASSIUM ION
3M7U2Ligand/Ion(2R)-2-(HEXADECANOYLOXY)-3-{[(10R)-10-METHYLOCTADECANOYL]OXY}PROPYL PHOSPHATE
4TLG2Ligand/Ion(5R)-3-ACETYL-4-HYDROXY-5-METHYL-5-[(1Z)-2-METHYLBUTA-1,3-DIEN-1-YL]THIOPHEN-2(5H)-ONE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:57 , SER A:211 , HOH A:2107 , HOH A:2109 , HOH A:2489 , PRO B:134 , ARG B:135BINDING SITE FOR RESIDUE EDO A1417
02AC2SOFTWAREASN A:309 , ALA A:310 , HIS A:311 , GLU A:354 , ASN A:399 , ASN A:400BINDING SITE FOR RESIDUE K A1418
03AC3SOFTWAREASN B:309 , ALA B:310 , HIS B:311 , GLU B:354 , ASN B:399 , ASN B:400BINDING SITE FOR RESIDUE K B1417
04AC4SOFTWAREALA A:18 , VAL A:19 , GLU A:30 , HOH A:2012 , HOH A:2491BINDING SITE FOR RESIDUE EDO A1419
05AC5SOFTWAREARG A:121 , GLU A:124 , SER A:125 , LEU A:128 , SER A:138BINDING SITE FOR RESIDUE EDO A1420
06AC6SOFTWAREVAL B:384 , VAL B:385 , ALA B:386 , ARG B:390 , HOH B:2384 , HOH B:2403BINDING SITE FOR RESIDUE EDO B1418
07AC7SOFTWAREPHE A:275 , PRO A:280 , ALA A:282 , ILE A:317 , TYR A:391 , HOH A:2409 , HOH A:2492BINDING SITE FOR RESIDUE EDO A1421
08AC8SOFTWAREALA A:282 , ASP A:283 , HOH A:2493 , HOH A:2494BINDING SITE FOR RESIDUE EDO A1422
09AC9SOFTWAREASP A:283 , VAL A:285 , HOH A:2377 , HOH A:2495 , ARG B:161BINDING SITE FOR RESIDUE EDO A1423
10BC1SOFTWARESER B:211 , ARG B:214 , ALA B:215 , MET B:216 , THR B:218BINDING SITE FOR RESIDUE EDO B1419
11BC2SOFTWARESER A:211 , ARG A:214 , ALA A:215 , MET A:216 , THR A:218 , ARG A:395 , HOH A:2299 , HOH A:2496BINDING SITE FOR RESIDUE EDO A1424
12BC3SOFTWAREARG A:79 , GLN A:84 , GLN A:143 , HOH A:2497BINDING SITE FOR RESIDUE EDO A1425
13BC4SOFTWAREASP A:69 , TYR A:82 , M7U A:1430 , HOH A:2118 , HOH A:2127BINDING SITE FOR RESIDUE EDO A1426
14BC5SOFTWAREARG A:74 , ARG A:78 , GLN B:333BINDING SITE FOR RESIDUE EDO B1420
15BC6SOFTWARETHR A:292 , GLU A:296 , LEU A:300 , PRO A:302 , HOH A:2391 , HOH A:2395 , HOH A:2500BINDING SITE FOR RESIDUE EDO A1427
16BC7SOFTWAREPRO B:201 , M7U B:1426 , HOH B:2125 , HOH B:2404BINDING SITE FOR RESIDUE EDO B1421
17BC8SOFTWARETYR A:126 , ASN A:130 , HOH A:2501 , HOH A:2502 , TRP B:54BINDING SITE FOR RESIDUE EDO A1428
18BC9SOFTWARETHR B:292 , GLU B:296 , LEU B:300 , HOH B:2319 , HOH B:2407BINDING SITE FOR RESIDUE EDO B1422
19CC1SOFTWARETRP A:54 , HOH A:2295 , TYR B:126 , ASN B:130 , HOH B:2408BINDING SITE FOR RESIDUE EDO B1423
20CC2SOFTWAREPRO A:134 , ARG A:135 , LEU B:56 , ALA B:57 , MET B:212 , HOH B:2090BINDING SITE FOR RESIDUE EDO B1424
21CC3SOFTWAREGLN A:171 , VAL A:278 , ALA A:279 , PRO A:280 , HIS A:311 , THR A:313 , HIS A:345 , PHE A:402 , GLY A:403 , PHE A:404 , GLY A:406 , HOH A:2274 , HOH A:2406BINDING SITE FOR RESIDUE TLG A1429
22CC4SOFTWAREGLN B:171 , PHE B:237 , VAL B:278 , ALA B:279 , PRO B:280 , HIS B:311 , THR B:313 , HIS B:345 , PHE B:402 , GLY B:403 , PHE B:404 , GLY B:406 , HOH B:2224 , HOH B:2336BINDING SITE FOR RESIDUE TLG B1425
23CC5SOFTWAREGLY A:115 , GLU A:120 , ALA A:170 , GLU A:199 , GLY A:200 , PRO A:201 , GLU A:203 , ALA A:209 , PHE A:239 , HIS A:345 , EDO A:1426 , HOH A:2221 , ILE B:145BINDING SITE FOR RESIDUE M7U A1430
24CC6SOFTWAREVAL A:142 , ILE A:145 , GLY B:115 , GLU B:120 , ALA B:170 , GLU B:199 , GLY B:200 , PRO B:201 , GLU B:203 , LEU B:205 , ALA B:209 , PHE B:239 , HIS B:345 , ILE B:347 , EDO B:1421 , HOH B:2125 , HOH B:2404BINDING SITE FOR RESIDUE M7U B1426

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C72)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C72)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C72)

(-) Exons   (0, 0)

(no "Exon" information available for 4C72)

(-) 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:413
 aligned with I6Y8T4_MYCTU | I6Y8T4 from UniProtKB/TrEMBL  Length:416

    Alignment length:413
                                    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   
         I6Y8T4_MYCTU     4 PSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
               SCOP domains d4c72a1 A:4-259 automated matches                                                                                                                                                                                                                               d4c72a2 A:260-416 automated matches                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee....hhhhhhhhhhh.....ee..hhhhhhhh....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeeeee....hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhh.........hhhhh...............eeeeeeeeehhhhhhhh....eeeeeeeeee...........hhhhhhhhhhhhhhhh.hhhhh.eee.....hhhhhhhhhhhhhhh.....eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhee...............ee.....ee....eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c72 A   4 PSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSAQSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
                                    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   


Chain B from PDB  Type:PROTEIN  Length:413
 aligned with I6Y8T4_MYCTU | I6Y8T4 from UniProtKB/TrEMBL  Length:416

    Alignment length:413
                                    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   
         I6Y8T4_MYCTU     4 PSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
               SCOP domains d4c72b1 B:4-259 automated matches                                                                                                                                                                                                                               d4c72b2 B:260-416 automated matches                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee....hhhhhhhhhhh.....ee..hhhhhhhh....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeeeee....hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhh........hhhhh...............eeeeeeeeehhhhhhhh....eeeeeeeeee...........hhhhhhhhhhhhhhhh.hhhhh.eee.....hhhhhhhhhhhhhhh.....eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhee...............ee.....ee....eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c72 B   4 PSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSAQSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
                                    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
   Legend:   → Mismatch (orange background)
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    → 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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C72)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C72)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (I6Y8T4_MYCTU | I6Y8T4)
molecular function
    GO:0033817    beta-ketoacyl-acyl-carrier-protein synthase II activity    Catalysis of the reaction: (Z)-hexadec-11-enoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = (Z)-3-oxooctadec-13-enoyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein].
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
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.

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  4c72
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  2.3.1.41
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 Related Entries

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

UniProtKB/TrEMBL
        I6Y8T4_MYCTU | I6Y8T4: 4c6u 4c6v 4c6w 4c6x 4c6z 4c70 4c71 4c73

(-) Related Entries Specified in the PDB File

4c6u CRYSTAL STRUCTURE OF M. TUBERCULOSIS KASA IN COMPLEX WITH TLM5
4c6v CRYSTAL STRUCTURE OF M. TUBERCULOSIS KASA IN COMPLEX WITH TLM5 (SOAK FOR 5 MIN)
4c6w CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA
4c6x CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH THIOLACTOMYCIN (TLM)
4c6z CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH TLM3
4c70 CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH TLM4
4c71 CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH TLM18
4c73 CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH TLM6