2AN9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF OLIGOMERIC E.COLI GUANYLATE KINASE IN COMPLEX WITH GDP

Authors :   G. Hible, L. Renault, F. Schaeffer, P. Christova, A. Z. Radulescu, C. Ev A. M. Gilles, J. Cherfils

Date :   11 Aug 05 (Deposition) - 30 Aug 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

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

Reference :   G. Hible, L. Renault, F. Schaeffer, P. Christova, A. Z. Radulescu, C. Evrin, A. M. Gilles, J. Cherfils
Calorimetric And Crystallographic Analysis Of The Oligomeri Structure Of Escherichia Coli Gmp Kinase
J. Mol. Biol. V. 352 1044 2005
PubMed-ID: 16140325 | Reference-DOI: 10.1016/J.JMB.2005.07.042

Molecule 1 - GUANYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BLI5
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GMK
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	GMP KINASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GMP	2	Ligand/Ion	GUANOSINE
3	K	2	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	GDP	6	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GMP	6	Ligand/Ion	GUANOSINE
3	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:38 , ASP A:102 , GDP A:601 , HOH A:623 , HOH A:625	BINDING SITE FOR RESIDUE K A 603
2	AC2	SOFTWARE	SER B:38 , ASP B:102 , GDP B:1601 , HOH B:1604 , HOH B:1605 , HOH B:1638	BINDING SITE FOR RESIDUE K B 1603
3	AC3	SOFTWARE	SER A:18 , SER A:38 , ARG A:42 , ARG A:45 , TYR A:54 , GLU A:73 , VAL A:77 , TYR A:82 , GLY A:83 , THR A:84 , ASP A:102 , ILE A:103 , ASP A:104 , GLY A:107 , K A:603 , HOH A:631 , HOH A:640 , HOH A:645 , HOH A:657 , HOH A:662 , HOH A:684	BINDING SITE FOR RESIDUE GDP A 601
4	AC4	SOFTWARE	LEU A:30 , TYR A:31 , GLN A:34 , THR A:95 , VAL A:97 , ARG A:133 , ARG A:134 , GLY A:137 , ARG A:138 , HOH A:615 , HOH A:626 , HOH A:634	BINDING SITE FOR RESIDUE GMP A 602
5	AC5	SOFTWARE	SER B:38 , ARG B:42 , ARG B:45 , TYR B:54 , GLU B:73 , TYR B:82 , GLY B:83 , THR B:84 , ASP B:102 , ILE B:103 , ASP B:104 , GLY B:107 , K B:1603 , HOH B:1637 , HOH B:1675 , HOH B:1676 , HOH B:1698	BINDING SITE FOR RESIDUE GDP B 1601
6	AC6	SOFTWARE	TYR B:31 , GLN B:34 , THR B:95 , VAL B:97 , ARG B:133 , ARG B:134 , GLY B:137 , ARG B:138 , HOH B:1624 , HOH B:1631 , HOH B:1670 , HOH B:1684	BINDING SITE FOR RESIDUE GMP B 1602

(no "SS Bond" information available for 2AN9)

(no "Cis Peptide Bond" information available for 2AN9)

(no "SAP(SNP)/Variant" information available for 2AN9)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GUANYLATE_KINASE_2	PS50052	Guanylate kinase-like domain profile.	KGUA_ECOLI	4-184	2	A:4-184 B:4-184
2	GUANYLATE_KINASE_1	PS00856	Guanylate kinase-like signature.	KGUA_ECOLI	40-57	2	A:40-57 B:40-57

Biological Unit 1 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GUANYLATE_KINASE_2	PS50052	Guanylate kinase-like domain profile.	KGUA_ECOLI	4-184	6	A:4-184 B:4-184
2	GUANYLATE_KINASE_1	PS00856	Guanylate kinase-like signature.	KGUA_ECOLI	40-57	6	A:40-57 B:40-57

(no "Exon" information available for 2AN9)

Asymmetric 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:205
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           KGUA_ECOLI     2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
               SCOP domains d2an9a_ A: Guanylate kinase                                                                                                                                                                                   SCOP domains
               CATH domains 2an9A01 A:2-36,A:97-206            2an9A02 A:37-96 Guanylate Kinase phosphate binding domain   2an9A01 A:2-36,A:97-206 P-loop containing nucleotide triphosphate hydrolases                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhh.....eee..eee.............eee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GUANYLATE_KINASE_2  PDB: A:4-184 UniProt: 4-184                                                                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------GUANYLATE_KINASE_1----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2an9 A   2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           KGUA_ECOLI     2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
               SCOP domains d2an9b_ B: Guanylate kinase                                                                                                                                                                                   SCOP domains
               CATH domains 2an9B01 B:2-36,B:97-206            2an9B02 B:37-96 Guanylate Kinase phosphate binding domain   2an9B01 B:2-36,B:97-206 P-loop containing nucleotide triphosphate hydrolases                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhh.....eee..eee.............eee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GUANYLATE_KINASE_2  PDB: B:4-184 UniProt: 4-184                                                                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------GUANYLATE_KINASE_1----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2an9 B   2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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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)

Escherichia coli [TaxId: 562] (6)

1a	d2an9a_	A:
1b	d2an9b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Guanylate Kinase phosphate binding domain (22)

Homologous Superfamily: Guanylate Kinase phosphate binding domain (22)

Escherichia coli. Organism_taxid: 562. (4)

1a	2an9A02	A:37-96
1b	2an9B02	B:37-96

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

Topology: Rossmann fold (7312)

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

Escherichia coli. Organism_taxid: 562. (54)

2a	2an9A01	A:2-36,A:97-206
2b	2an9B01	B:2-36,B:97-206

(no "Pfam Domain" information available for 2AN9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KGUA_ECOLI | P60546)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.
	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 Unit
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Biological Unit
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	KGUA_ECOLI \| P60546	:	1s96 2anb 2anc 2f3r 2f3t

2anb	CRYSTAL STRUCTURE OF OLIGOMERIC E.COLI GUANYLATE KINASE IN COMPLEX WITH GMP
2anc	CRYSTAL STRUCTURE OF UNLIGANDED FORM OF OLIGOMERIC E.COLI GUANYLATE KINASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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