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(-) Description

Title :  CRYSTAL STRUCTURE OF KASA OF MYCOBACTERIUM TUBERCULOSIS
 
Authors :  S. R. Luckner, C. Kisker
Date :  17 Apr 09  (Deposition) - 21 Jul 09  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Beta Ketoacyl Synthase I, Cytoplasm, Transferase, Acyltransferase, Lipid Synthesis, Fatty Acid Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. R. Luckner, C. A. Machutta, P. J. Tonge, C. Kisker
Crystal Structures Of Mycobacterium Tuberculosis Kasa Show Mode Of Action Within Cell Wall Biosynthesis And Its Inhibition By Thiolactomycin
Structure V. 17 1004 2009
PubMed-ID: 19604480  |  Reference-DOI: 10.1016/J.STR.2009.04.012

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
    ChainsA
    EC Number2.3.1.41
    EngineeredYES
    Expression SystemMYCOBACTERIUM SMEGMATIS
    Expression System StrainMC2155
    Expression System Taxid1772
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    SynonymBETA KETOACYL SYNTHASE I, KAS 1, BETA-KETOACYL-ACP SYNTHASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2IPA1Ligand/IonISOPROPYL ALCOHOL
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2IPA2Ligand/IonISOPROPYL ALCOHOL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:275 , ALA A:282 , ASP A:283 , HOH A:2178 , HOH A:2179BINDING SITE FOR RESIDUE GOL A1416
2AC2SOFTWAREALA A:18 , VAL A:19 , GLU A:30 , ARG A:363 , HOH A:2180 , HOH A:2181BINDING SITE FOR RESIDUE GOL A1417
3AC3SOFTWAREGLU A:199 , GLY A:200 , PRO A:201 , ILE A:202 , GLU A:203 , PRO A:206 , PHE A:239 , SER A:346 , HOH A:2182BINDING SITE FOR RESIDUE GOL A1418
4AC4SOFTWAREMET A:213 , ILE A:317 , HOH A:2138 , HOH A:2183BINDING SITE FOR RESIDUE IPA A1419
5AC5SOFTWAREASN A:309 , ALA A:310 , GLU A:354 , ASN A:399 , ASN A:400BINDING SITE FOR RESIDUE NA A1420
6AC6SOFTWAREARG A:289 , THR A:292 , VAL A:328BINDING SITE FOR RESIDUE GOL A1421

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WGD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WGD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WGD)

(-) 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:415
 aligned with FAB1_MYCTO | P9WQD8 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:415
                                    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       361       371       381       391       401       411     
           FAB1_MYCTO     2 SQPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
               SCOP domains d2wgda1 A:2-259 automated matches                                                                                                                                                                                                                                 d2wgda2 A:260-416 automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------ketoacyl-synt-2wgdA02 A:11-254                                                                                                                                                                                                                      -------Ketoacyl-synt_C-2wgdA01 A:262-374                                                                                ------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeeeeee....hhhhhhhhhhh.....ee..hhhhhhhh....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeeeeee......hhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhh.........hhhhh...............eeeeeeeeehhhhhhh.....eeeeeeeeee...........hhhhhhhhhhhhhhhh.hhhhh.eee.....hhhhhhhhhhhhhhh.....eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhee...............ee.....ee....eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wgd A   2 SQPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
                                    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       361       371       381       391       401       411     

Chain A from PDB  Type:PROTEIN  Length:415
 aligned with FAB1_MYCTU | P9WQD9 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:415
                                    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       361       371       381       391       401       411     
           FAB1_MYCTU     2 SQPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
               SCOP domains d2wgda1 A:2-259 automated matches                                                                                                                                                                                                                                 d2wgda2 A:260-416 automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------ketoacyl-synt-2wgdA02 A:11-254                                                                                                                                                                                                                      -------Ketoacyl-synt_C-2wgdA01 A:262-374                                                                                ------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeeeeee....hhhhhhhhhhh.....ee..hhhhhhhh....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeeeeee......hhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhh.........hhhhh...............eeeeeeeeehhhhhhh.....eeeeeeeeee...........hhhhhhhhhhhhhhhh.hhhhh.eee.....hhhhhhhhhhhhhhh.....eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhee...............ee.....ee....eeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wgd A   2 SQPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
                                    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       361       371       381       391       401       411     

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Thiolase (72)

(-) Gene Ontology  (16, 25)

Asymmetric Unit(hide GO term definitions)
Chain A   (FAB1_MYCTO | P9WQD8)
molecular function
    GO:0004315    3-oxoacyl-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[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:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (FAB1_MYCTU | P9WQD9)
molecular function
    GO:0004315    3-oxoacyl-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0030497    fatty acid elongation    The elongation of a fatty acid chain by the sequential addition of two-carbon units.
    GO:0019367    fatty acid elongation, saturated fatty acid    Elongation of a saturated fatty acid chain.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FAB1_MYCTO | P9WQD82wge 2wgf 2wgg
        FAB1_MYCTU | P9WQD92wge 2wgf 2wgg 5ld8

(-) Related Entries Specified in the PDB File

2wge CRYSTAL STRUCTURE OF KASA OF MYCOBACTERIUM TUBERCULOSIS WITH BOUND TLM
2wgf CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS C171Q KASA VARIANT
2wgg CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS C171Q KASA VARIANT WITH BOUND TLM