3T44 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS INDOLE GLYCEROL PHOSPHATE SYNTHASE (IGPS) IN COMPLEX WITH INDOLE GLYCEROL PHOSPHATE (IGP) AMD ANTHRANILATE

Authors :   M. C. M. Reddy, J. B. Bruning, C. Thurman, J. C. Sacchettini, Tb Structu Genomics Consortium (Tbsgc)

Date :   25 Jul 11 (Deposition) - 08 Aug 12 (Release) - 08 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Mycobacterium Tuberculosis Indole Glycerol Phosphate Synthase (Igps), Tryptophan Biosynthesis, Structural Genomics, Tb Structural Genomics Consortium, Tbsgc, Transferase (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

Molecule 1 - INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
	Chains	:	A
	EC Number	:	4.1.1.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	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

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	BE2	1	Ligand/Ion	2-AMINOBENZOIC ACID
2	IGP	1	Ligand/Ion	INDOLE-3-GLYCEROL PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:57 , LYS A:59 , LYS A:119 , PHE A:121 , LEU A:140 , GLU A:168 , ASN A:189 , GLU A:219 , SER A:220 , GLY A:221 , LEU A:240 , VAL A:241 , GLY A:242 , GLU A:243 , BE2 A:273 , HOH A:346 , HOH A:358 , HOH A:378 , HOH A:551	BINDING SITE FOR RESIDUE IGP A 300
2	AC2	SOFTWARE	SER A:62 , PRO A:63 , SER A:64 , PHE A:98 , ARG A:191 , LEU A:193 , LEU A:196 , IGP A:300 , HOH A:396 , HOH A:450	BINDING SITE FOR RESIDUE BE2 A 273

(no "SS Bond" information available for 3T44)

(no "Cis Peptide Bond" information available for 3T44)

(no "SAP(SNP)/Variant" information available for 3T44)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IGPS	PS00614	Indole-3-glycerol phosphate synthase signature.	TRPC_MYCTO	54-71	1	A:54-71
1	IGPS	PS00614	Indole-3-glycerol phosphate synthase signature.	TRPC_MYCTU	54-71	1	A:54-71

(no "Exon" information available for 3T44)

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:259
 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.....hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh..eeeee..........hhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------IGPS  PDB: A:54-71------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t44 A   5 TVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALREPGIGVIAEVKRASPSAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVVQPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKAGAKVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEGLVTSGDPRAAVADLVTAGT 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

Chain A from PDB  Type:PROTEIN  Length:259
 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.....hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh..eeeee..........hhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------IGPS  PDB: A:54-71------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t44 A   5 TVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALREPGIGVIAEVKRASPSAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVVQPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKAGAKVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEGLVTSGDPRAAVADLVTAGT 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

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 '\|'

(no "SCOP Domain" information available for 3T44)

(no "CATH Domain" information available for 3T44)

(no "Pfam Domain" information available for 3T44)

Asymmetric/Biological Unit(hide GO term definitions)

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.

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.

Asymmetric/Biological Unit
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	3t44
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	TRPC_MYCTU \| P9WFX7
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	4.1.1.48
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UniProtKB/Swiss-Prot
	TRPC_MYCTO \| P9WFX6	:	3qja 3t40 3t55 3t78 4fb7
	TRPC_MYCTU \| P9WFX7	:	3qja 3t40 3t55 3t78 4fb7

3qja	APO STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS INDOLE GLYCEROL PHOSPHATE SYNTHASE (IGPS)
3t40
3t55
3t78

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (15, 24)

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