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Asym./Biol. Unit (Jmol Viewer)

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

Title :   SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SHIKIMATE, OPEN LID (CONF. A)

Authors :   M. D. Hartmann, G. P. Bourenkov, A. Oberschall, N. Strizhov, H. D. Bartunik

Date :   21 Jul 06 (Deposition) - 11 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Transferase, Aromatic Amino Acid Biosynthesis, P-Loop Kinase, Metal- Binding, Shikimate Kinase, Shikimate Pathway, Nucleotide- Binding, Amino-Acid Biosynthesis, Kinase, Magnesium, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. D. Hartmann, G. P. Bourenkov, A. Oberschall, N. Strizhov, H. D. Bartunik
Mechanism Of Phosphoryl Transfer Catalyzed By Shikimate Kinase From Mycobacterium Tuberculosis.
J. Mol. Biol. V. 364 411 2006
PubMed-ID: 17020768 | Reference-DOI: 10.1016/J.JMB.2006.09.001

Molecule 1 - SHIKIMATE KINASE
	Atcc	:	25618
	Chains	:	A
	EC Number	:	2.7.1.71
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	SK

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	SKM	1	Ligand/Ion	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:21 , HOH A:2014	BINDING SITE FOR RESIDUE CL A 202
2	AC2	SOFTWARE	ASP A:34 , ALA A:46 , ALA A:50 , ARG A:58 , GLY A:79 , GLY A:80 , GLY A:81 , ARG A:136 , HOH A:2161 , HOH A:2162 , HOH A:2163 , HOH A:2164 , HOH A:2165 , HOH A:2167 , HOH A:2168	BINDING SITE FOR RESIDUE SKM A 201

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

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

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIKIMATE_KINASE	PS01128	Shikimate kinase signature.	AROK_MYCTO	58-83	1	A:58-83
1	SHIKIMATE_KINASE	PS01128	Shikimate kinase signature.	AROK_MYCTU	58-83	1	A:58-83

(no "Exon" information available for 2IYS)

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:175
 aligned with AROK_MYCTO | P9WPY2 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
           AROK_MYCTO     2 APKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGGNTVRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRLQVPSPSEAAT 176
               SCOP domains d2iysa_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains 2iysA00 A:2-176 P-loop containing nucleotide triphosphate hydrolases                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh...eeeee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------SHIKIMATE_KINASE          --------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iys A   2 APKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGGNTVRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRLQVPSPSEAAT 176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain A from PDB  Type:PROTEIN  Length:175
 aligned with AROK_MYCTU | P9WPY3 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
           AROK_MYCTU     2 APKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGGNTVRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRLQVPSPSEAAT 176
               SCOP domains d2iysa_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains 2iysA00 A:2-176 P-loop containing nucleotide triphosphate hydrolases                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh...eeeee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------SHIKIMATE_KINASE          --------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iys A   2 APKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGGNTVRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRLQVPSPSEAAT 176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Shikimate kinase (AroK) (26)

Protein domain: automated matches (10)

Mycobacterium tuberculosis [TaxId: 83332] (10)

d2iysa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. (16)

2iysA00

A:2-176

(no "Pfam Domain" information available for 2IYS)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (AROK_MYCTO | P9WPY2)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004765	shikimate kinase activity	Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H(+).
	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.
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:0009423	chorismate biosynthetic process	The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
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 (AROK_MYCTU | P9WPY3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004765	shikimate kinase activity	Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H(+).
	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.
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:0009423	chorismate biosynthetic process	The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0019632	shikimate metabolic process	The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.
cellular component
	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.

Asymmetric/Biological Unit
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1l4u	CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUMTUBERCULOSIS IN COMPLEX WITH MGADP AND PT(II) AT 1.8ANGSTROM RESOLUTION
1l4y	CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUMTUBERCULOSIS IN COMPLEX WITH MGADP AT 2.0 ANGSTROMRESOLUTION
1u8a	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS SHIKIMATEKINASE IN COMPLEX WITH SHIKIMATE AND ADP AT 2.15 ANGSTROMRESOLUTION
1zyu	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS SHIKIMATEKINASE IN COMPLEX WITH SHIKIMATE AND AMPPCP AT 2.85ANGSTROM RESOLUTION
2g1j	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS SHIKIMATEKINASE AT 2.0 ANGSTROM RESOLUTION
2g1k	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS SHIKIMATEKINASE IN COMPLEX WITH SHIKIMATE AT 1.75 ANGSTROMRESOLUTION
2iyq	SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SHIKIMATE AND ADP
2iyr	SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SHIKIMATE
2iyt	SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN UNLIGANDED STATE, OPEN LID (CONF. A)
2iyu	SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH ADP, OPEN LID (CONF. A)
2iyv	SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH ADP, OPEN LID (CONF. B)
2iyw	SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGATP, OPEN LID (CONF. B)
2iyx	SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SHIKIMATE AND SO4
2iyy	SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SHIKIMATE-3-PHOSPHATE AND SO4
2iyz	SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SHIKIMATE-3-PHOSPHATE AND ADP

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

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (15, 27)

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Related Entries

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Related Entries Specified in the PDB File