1S4Q - JenaLib

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Title :   CRYSTAL STRUCTURE OF GUANYLATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS (RV1389)

Authors :   S. Chan, M. R. Sawaya, L. J. Perry, D. Eisenberg, Tb Structural Genomi Consortium (Tbsgc)

Date :   16 Jan 04 (Deposition) - 27 Jan 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.16

Chains :   Asym./Biol. Unit : A

Keywords :   Transferase, Atp:Gmp-Phosphotransferase, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chan, M. R. Sawaya, L. J. Perry, D. Eisenberg
Crystal Structure Of Guanylate Kinase From Mycobacterium Tuberculosis
To Be Published
PubMed: search

Molecule 1 - GUANYLATE KINASE
	Chains	:	A
	EC Number	:	2.7.4.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21-GOLD (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GMK, RV1389, MT1434, MTCY21B4.06, MB1424
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	GMP KINASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	FMT	3	Ligand/Ion	FORMIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:179	BINDING SITE FOR RESIDUE CL A 300
2	AC2	SOFTWARE	ALA A:31 , VAL A:32 , GLY A:33 , LYS A:34 , SER A:35	BINDING SITE FOR RESIDUE FMT A 301
3	AC3	SOFTWARE	ARG A:42 , LEU A:48 , HIS A:49 , PHE A:50 , GLN A:146 , GLN A:149 , ALA A:150 , HOH A:353	BINDING SITE FOR RESIDUE FMT A 302
4	AC4	SOFTWARE	HIS A:93 , ASP A:161 , ARG A:165 , ASP A:168	BINDING SITE FOR RESIDUE FMT A 303

Asymmetric/Biological Unit

No.	Residues
1	A:40	-	A:193

(no "Cis Peptide Bond" information available for 1S4Q)

(no "SAP(SNP)/Variant" information available for 1S4Q)

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 1S4Q)

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 d1s4qa_ A: Guanylate kinase                                                                                                                                                             SCOP domains
               CATH domains 1s4qA01 A:20-51,A:115-202       1s4qA02 A:52-114 Guanylate Kinase phosphate binding domain     1s4qA01 A:20-51,A:115-202 P-loop containing nucleotide triphosphate hydrolases           CATH domains
               Pfam domains Guanylate_kin-1s4qA01 A:20-202                                                                                                                                                          Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhh...ee...ee..............ee.hhhhhhhhhhh..eeeeeee....eeeeeehhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhh. 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
                 1s4q 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 d1s4qa_ A: Guanylate kinase                                                                                                                                                             SCOP domains
               CATH domains 1s4qA01 A:20-51,A:115-202       1s4qA02 A:52-114 Guanylate Kinase phosphate binding domain     1s4qA01 A:20-51,A:115-202 P-loop containing nucleotide triphosphate hydrolases           CATH domains
               Pfam domains Guanylate_kin-1s4qA01 A:20-202                                                                                                                                                          Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhh...ee...ee..............ee.hhhhhhhhhhh..eeeeeee....eeeeeehhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhh. 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
                 1s4q 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: Guanylate kinase (13)

Mycobacterium tuberculosis [TaxId: 1773] (2)

d1s4qa_

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Guanylate_kin (23)

Mycobacterium tuberculosis (5)

Guanylate_kin-1s4qA01

A:20-202

Asymmetric/Biological Unit(hide GO term definitions)

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.

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.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1S4Q)

Description

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (1, 1)

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