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 MYCOBACTERIUM TUBERCULOSIS INDOLE GLYCEROL PHOSPHATE SYNTHASE (IGPS) IN COMPLEX WITH 5-FLUOROANTHRANILATE
 
Authors :  M. C. M. Reddy, J. B. Bruning, C. Thurman, J. C. Sacchettini, Tb Structu Genomics Consortium (Tbsgc)
Date :  29 Jul 11  (Deposition) - 08 Aug 12  (Release) - 08 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Indole-3-Glycerol Phosphate Synthase (Igps), Tryptophan Biosynthesis, Structural Genomics, Tb Structural Genomics Consortium, Tbsgc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. M. Reddy, J. B. Bruning, C. Thurman, J. C. Sacchettini
Structural Insights And Inhibition Of Mycobacterium Tuberculosis Indole Glycerol Phosphate Synthase (Igps): An Essential Enzyme For Tryptophan Biosynthesis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
    Chains: A
    EC Number: 4.1.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MT1646, MTCY01B2.03, RV1611, TRPC
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: IGPS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
15RG1Ligand/Ion2-AMINO-5-FLUOROBENZOIC ACID
2ACT3Ligand/IonACETATE ION
3MLI1Ligand/IonMALONATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:59 , SER A:62 , PRO A:63 , SER A:64 , PHE A:98 , PHE A:121 , ARG A:191 , LEU A:193 , LEU A:196 , MLI A:274 , ACT A:275BINDING SITE FOR RESIDUE 5RG A 273
2AC2SOFTWARELYS A:59 , ARG A:191 , GLU A:219 , SER A:220 , GLY A:242 , GLU A:243 , 5RG A:273 , HOH A:377 , HOH A:379 , HOH A:406 , HOH A:523 , HOH A:621BINDING SITE FOR RESIDUE MLI A 274
3AC3SOFTWAREPHE A:98 , LYS A:119 , PHE A:121 , 5RG A:273 , HOH A:491BINDING SITE FOR RESIDUE ACT A 275
4AC4SOFTWARELYS A:31 , PRO A:74 , ASP A:103 , ASP A:104 , ARG A:157BINDING SITE FOR RESIDUE ACT A 276
5AC5SOFTWAREARG A:200 , GLY A:221 , ARG A:223 , ASP A:227 , HOH A:510BINDING SITE FOR RESIDUE ACT A 277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T78)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T78)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T78)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IGPSPS00614 Indole-3-glycerol phosphate synthase signature.TRPC_MYCTO54-71  1A:54-71
TRPC_MYCTU54-71  1A:54-71

(-) Exons   (0, 0)

(no "Exon" information available for 3T78)

(-) 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:257
 aligned with TRPC_MYCTO | P9WFX6 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:259
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
           TRPC_MYCTO     5 TVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALREPGIGVIAEVKRASPSAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVVQPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMIALVEVHTEQEADRALKAGAKVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEGLVTSGDPRAAVADLVTAGT 263
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....eeeeee..ee...ee.....hhhhhhhhhhhh...eeeee........hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh..eeee.........--.hhhhhhhhhh....eeee.....hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------IGPS  PDB: A:54-71------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t78 A   5 TVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALREPGIGVIAEVKRASPSAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVVQPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKAGAKVIGVNARDLMTLD--RDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEGLVTSGDPRAAVADLVTAGT 263
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  |  | 204       214       224       234       244       254         
                                                                                                                                                                                                                          197  |                                                               
                                                                                                                                                                                                                             200                                                               


Chain A from PDB  Type:PROTEIN  Length:257
 aligned with TRPC_MYCTU | P9WFX7 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:259
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
           TRPC_MYCTU     5 TVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALREPGIGVIAEVKRASPSAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVVQPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKAGAKVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEGLVTSGDPRAAVADLVTAGT 263
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....eeeeee..ee...ee.....hhhhhhhhhhhh...eeeee........hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh..eeee.........--.hhhhhhhhhh....eeee.....hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------IGPS  PDB: A:54-71------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t78 A   5 TVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALREPGIGVIAEVKRASPSAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVVQPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKAGAKVIGVNARDLMTLD--RDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEGLVTSGDPRAAVADLVTAGT 263
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  |  | 204       214       224       234       244       254         
                                                                                                                                                                                                                          197  |                                                               
                                                                                                                                                                                                                             200
   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  (0, 0)

(no "SCOP Domain" information available for 3T78)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T78)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T78)

(-) Gene Ontology  (15, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRPC_MYCTO | P9WFX6)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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:0004425    indole-3-glycerol-phosphate synthase activity    Catalysis of the reaction: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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.
    GO:0000162    tryptophan biosynthetic process    The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.

Chain A   (TRPC_MYCTU | P9WFX7)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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:0004425    indole-3-glycerol-phosphate synthase activity    Catalysis of the reaction: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0004640    phosphoribosylanthranilate isomerase activity    Catalysis of the reaction: N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate.
biological process
    GO:0046391    5-phosphoribose 1-diphosphate metabolic process    The chemical reactions and pathways involving 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    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.
    GO:0000162    tryptophan biosynthetic process    The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
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: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.

 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
    5RG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLI  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3t78)
 

(-) 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
  3t78
    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
  TRPC_MYCTO | P9WFX6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TRPC_MYCTU | P9WFX7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.48
    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
  TRPC_MYCTO | P9WFX6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TRPC_MYCTU | P9WFX7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TRPC_MYCTO | P9WFX6: 3qja 3t40 3t44 3t55 4fb7
        TRPC_MYCTU | P9WFX7: 3qja 3t40 3t44 3t55 4fb7

(-) Related Entries Specified in the PDB File

3qja APO CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS INDOLE GLYCEROL PHOSPHATE SYNTHASE (IGPS)
3t40
3t44
3t55