Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH TLM4
 
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 :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, 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  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2IPA4Ligand/IonISOPROPYL ALCOHOL
3K2Ligand/IonPOTASSIUM ION
4M7U2Ligand/Ion(2R)-2-(HEXADECANOYLOXY)-3-{[(10R)-10-METHYLOCTADECANOYL]OXY}PROPYL PHOSPHATE
5TLJ2Ligand/Ion(5R)-4-HYDROXY-5-METHYL-5-[(1E)-2-METHYLBUTA-1,3-DIEN-1-YL]-3-PROPYLTHIOPHEN-2(5H)-ONE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:18 , VAL A:19 , GLU A:30 , ARG A:363 , HOH A:2018 , HOH A:2381 , HOH A:2424BINDING SITE FOR RESIDUE GOL A1417
02AC2SOFTWARETYR A:126 , ASN A:130 , HOH A:2425 , HOH B:2206BINDING SITE FOR RESIDUE IPA A1418
03AC3SOFTWAREASP A:69 , TYR A:82 , M7U A:1424 , HOH A:2122BINDING SITE FOR RESIDUE IPA A1419
04AC4SOFTWARESER A:211 , ARG A:214 , ALA A:215 , MET A:216 , ASP A:393 , HOH A:2275BINDING SITE FOR RESIDUE GOL A1420
05AC5SOFTWAREASP A:283 , VAL A:285 , HOH A:2157 , HOH A:2312 , HOH A:2332 , HOH A:2426 , HOH A:2427 , ARG B:161 , HOH B:2144BINDING SITE FOR RESIDUE IPA A1421
06AC6SOFTWAREASN A:309 , ALA A:310 , HIS A:311 , GLU A:354 , ASN A:399 , ASN A:400BINDING SITE FOR RESIDUE K A1422
07AC7SOFTWAREASN B:309 , ALA B:310 , HIS B:311 , GLU B:354 , ASN B:399 , ASN B:400BINDING SITE FOR RESIDUE K B1417
08AC8SOFTWAREALA B:18 , VAL B:19 , ILE B:29 , GLU B:30 , HOH B:2016 , HOH B:2309 , HOH B:2341BINDING SITE FOR RESIDUE GOL B1418
09AC9SOFTWARESER B:211 , ARG B:214 , ALA B:215 , MET B:216BINDING SITE FOR RESIDUE IPA B1419
10BC1SOFTWAREGLN A:171 , PHE A:237 , 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:2321 , HOH A:2356 , HOH A:2428BINDING SITE FOR RESIDUE TLJ A1423
11BC2SOFTWAREGLN B:171 , PHE B:237 , HIS B:276 , VAL B:278 , ALA B:279 , PRO B:280 , HIS B:311 , THR B:313 , HIS B:345 , PHE B:402 , GLY B:406 , HOH B:2285 , HOH B:2342BINDING SITE FOR RESIDUE TLJ B1420
12BC3SOFTWARETYR A:82 , GLY A:115 , GLU A:120 , ALA A:170 , GLU A:199 , GLY A:200 , PRO A:201 , GLU A:203 , LEU A:205 , ALA A:209 , HIS A:345 , IPA A:1419 , VAL B:142 , ILE B:145BINDING SITE FOR RESIDUE M7U A1424
13BC4SOFTWAREVAL 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 , ALA B:209 , HIS B:345 , ILE B:347BINDING SITE FOR RESIDUE M7U B1421

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C70)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C70)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C70)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C70)

(-) Exons   (0, 0)

(no "Exon" information available for 4C70)

(-) 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:415
 aligned with I6Y8T4_MYCTU | I6Y8T4 from UniProtKB/TrEMBL  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     
         I6Y8T4_MYCTU     2 SQPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
               SCOP domains d4c70a1 A:2-259 automated matches                                                                                                                                                                                                                                 d4c70a2 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
                 4c70 A   2 SQPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSAQSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 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 B from PDB  Type:PROTEIN  Length:414
 aligned with I6Y8T4_MYCTU | I6Y8T4 from UniProtKB/TrEMBL  Length:416

    Alignment length:414
                                    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       342       352       362       372       382       392       402       412    
         I6Y8T4_MYCTU     3 QPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
               SCOP domains d4c70b1 B:3-259 automated matches                                                                                                                                                                                                                                d4c70b2 B:260-416 automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeee....hhhhhhhhhhh.....ee..hhhhhhh.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeeeee....hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh....eeeeee.....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
                 4c70 B   3 QPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSAQSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY 416
                                    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       342       352       362       372       382       392       402       412
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C70)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C70)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IPA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    M7U  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TLJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4c70)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4c70
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  I6Y8T4_MYCTU | I6Y8T4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.3.1.41
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  I6Y8T4_MYCTU | I6Y8T4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        I6Y8T4_MYCTU | I6Y8T4: 4c6u 4c6v 4c6w 4c6x 4c6z 4c71 4c72 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
4c71 CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH TLM18
4c72 CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH TLM5
4c73 CRYSTAL STRUCTURE OF M. TUBERCULOSIS C171Q KASA IN COMPLEX WITH TLM6