1ZNY - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GUANYLATE KINASE IN COMPLEX WITH GDP

Authors :   G. Hible, P. Christova, L. Renault, E. Seclaman, A. Thompson, E. Girard H. Munier-Lehmann, J. Cherfils

Date :   12 May 05 (Deposition) - 29 Nov 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Guanylate Kinase, Gmp Kinase, Atp:Gmp-Phosphotransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Hible, P. Christova, L. Renault, E. Seclaman, A. Thompson, E. Girard, H. Munier-Lehmann, J. Cherfils
Unique Gmp-Binding Site In Mycobacterium Tuberculosis Guanosine Monophosphate Kinase
Proteins V. 62 489 2006
PubMed-ID: 16288457 | Reference-DOI: 10.1002/PROT.20662

Molecule 1 - GUANYLATE KINASE
	Chains	:	A
	EC Number	:	2.7.4.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GMK (RV1389)
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	GMP KINASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:53 , ARG A:57 , ARG A:60 , TYR A:69 , GLU A:88 , GLY A:100 , HOH A:319 , HOH A:347	BINDING SITE FOR RESIDUE GDP A 300

Asymmetric/Biological Unit

No.	Residues
1	A:40	-	A:193

(no "Cis Peptide Bond" information available for 1ZNY)

(no "SAP(SNP)/Variant" information available for 1ZNY)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GUANYLATE_KINASE_2	PS50052	Guanylate kinase-like domain profile.	KGUA_MYCTO	21-201	1	A:21-201
1	GUANYLATE_KINASE_2	PS50052	Guanylate kinase-like domain profile.	KGUA_MYCTU	21-201	1	A:21-201
2	GUANYLATE_KINASE_1	PS00856	Guanylate kinase-like signature.	KGUA_MYCTO	55-72	1	A:55-72
2	GUANYLATE_KINASE_1	PS00856	Guanylate kinase-like signature.	KGUA_MYCTU	55-72	1	A:55-72

(no "Exon" information available for 1ZNY)

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:183
 aligned with KGUA_MYCTO | P9WKE8 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:183
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   
           KGUA_MYCTO    20 VGRVVVLSGPSAVGKSTVVRCLRERIPNLHFSVSATTRAPRPGEVDGVDYHFIDPTRFQQLIDQGELLEWAEIHGGLHRSGTLAQPVRAAAATGVPVLIEVDLAGARAIKKTMPEAVTVFLAPPSWQDLQARLIGRGTETADVIQRRLDTARIELAAQGDFDKVVVNRRLESACAELVSLLVG 202
               SCOP domains d1znya_ A: automated matches                                                                                                                                                            SCOP domains
               CATH domains 1znyA01 A:20-51,A:115-202       1znyA02 A:52-114 Guanylate Kinase phosphate binding domain     1znyA01 A:20-51,A:115-202 P-loop containing nucleotide triphosphate hydrolases           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhh...ee...ee..............ee.hhhhhhhhhhh..eeeeeee....eeeeeehhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GUANYLATE_KINASE_2  PDB: A:21-201 UniProt: 21-201                                                                                                                                    - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------GUANYLATE_KINASE_1---------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zny A  20 VGRVVVLSGPSAVGKSTVVRCLRERIPNLHFSVSATTRAPRPGEVDGVDYHFIDPTRFQQLIDQGELLEWAEIHGGLHRSGTLAQPVRAAAATGVPVLIEVDLAGARAIKKTMPEAVTVFLAPPSWQDLQARLIGRGTETADVIQRRLDTARIELAAQGDFDKVVVNRRLESACAELVSLLVG 202
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199

Chain A from PDB  Type:PROTEIN  Length:183
 aligned with KGUA_MYCTU | P9WKE9 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:183
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   
           KGUA_MYCTU    20 VGRVVVLSGPSAVGKSTVVRCLRERIPNLHFSVSATTRAPRPGEVDGVDYHFIDPTRFQQLIDQGELLEWAEIHGGLHRSGTLAQPVRAAAATGVPVLIEVDLAGARAIKKTMPEAVTVFLAPPSWQDLQARLIGRGTETADVIQRRLDTARIELAAQGDFDKVVVNRRLESACAELVSLLVG 202
               SCOP domains d1znya_ A: automated matches                                                                                                                                                            SCOP domains
               CATH domains 1znyA01 A:20-51,A:115-202       1znyA02 A:52-114 Guanylate Kinase phosphate binding domain     1znyA01 A:20-51,A:115-202 P-loop containing nucleotide triphosphate hydrolases           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhh...ee...ee..............ee.hhhhhhhhhhh..eeeeeee....eeeeeehhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GUANYLATE_KINASE_2  PDB: A:21-201 UniProt: 21-201                                                                                                                                    - PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------------------------GUANYLATE_KINASE_1---------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zny A  20 VGRVVVLSGPSAVGKSTVVRCLRERIPNLHFSVSATTRAPRPGEVDGVDYHFIDPTRFQQLIDQGELLEWAEIHGGLHRSGTLAQPVRAAAATGVPVLIEVDLAGARAIKKTMPEAVTVFLAPPSWQDLQARLIGRGTETADVIQRRLDTARIELAAQGDFDKVVVNRRLESACAELVSLLVG 202
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199

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: Nucleotide and nucleoside kinases (231)

Protein domain: automated matches (25)

Mycobacterium tuberculosis [TaxId: 1773] (6)

d1znya_

(no "Pfam Domain" information available for 1ZNY)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (KGUA_MYCTO | P9WKE8)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004385	guanylate kinase activity	Catalysis of the reaction: ATP + GMP = ADP + GDP.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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:0046710	GDP metabolic process	The chemical reactions and pathways involving GDP, guanosine 5'-diphosphate.
	GO:0046037	GMP metabolic process	The chemical reactions and pathways involving GMP, guanosine monophosphate.
	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:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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 (KGUA_MYCTU | P9WKE9)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019003	GDP binding	Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
	GO:0019002	GMP binding	Interacting selectively and non-covalently with GMP, guanosine monophosphate.
	GO:0004017	adenylate kinase activity	Catalysis of the reaction: ATP + AMP = 2 ADP.
	GO:0004385	guanylate kinase activity	Catalysis of the reaction: ATP + GMP = ADP + GDP.
	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: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: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:0046710	GDP metabolic process	The chemical reactions and pathways involving GDP, guanosine 5'-diphosphate.
	GO:0046037	GMP metabolic process	The chemical reactions and pathways involving GMP, guanosine monophosphate.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0046939	nucleotide phosphorylation	The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
	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:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	1zny
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	KGUA_MYCTO \| P9WKE8
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	KGUA_MYCTU \| P9WKE9
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	2.7.4.8
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UniProtKB/Swiss-Prot
	KGUA_MYCTO \| P9WKE8	:	1s4q 1z8f 1znw 1znx 1znz
	KGUA_MYCTU \| P9WKE9	:	1s4q 1z8f 1znw 1znx 1znz

1znw	CRYSTAL STRUCTURE OF THE M.TUBERCULOSIS PROTEIN WITH NO LIGAND
1znx	CRYSTAL STRUCTURE OF THE M.TUBERCULOSIS PROTEIN LIGANDED WITH GMP
1znz	CRYSTAL STRUCTURE OF THE REDUCED FORM OF THE M.TUBERCULOSIS PROTEIN LIGANDED WITH GDP

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (16, 26)

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