1EX6 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF UNLIGANDED FORM OF GUANYLATE KINASE FROM YEAST

Authors :   J. Blaszczyk, X. Ji

Date :   01 May 00 (Deposition) - 16 Mar 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Guanylate Kinase, Substrate-Induced Fit, Domain Movement, Atp, Gmp, Substrate Specificity, X-Ray Diffraction, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Blaszczyk, Y. Li, H. Yan, X. Ji
Crystal Structure Of Unligated Guanylate Kinase From Yeast Reveals Gmp-Induced Conformational Changes.
J. Mol. Biol. V. 307 247 2001
PubMed-ID: 11243817 | Reference-DOI: 10.1006/JMBI.2000.4427
(for further references see the PDB file header)

Molecule 1 - GUANYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1EX6)

(no "Site" information available for 1EX6)

(no "SS Bond" information available for 1EX6)

(no "Cis Peptide Bond" information available for 1EX6)

(no "SAP(SNP)/Variant" information available for 1EX6)

Asymmetric/Biological 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_YEAST	2-184	2	A:1-183 B:201-383
2	GUANYLATE_KINASE_1	PS00856	Guanylate kinase-like signature.	KGUA_YEAST	37-54	2	A:36-53 B:236-253

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR454C	1	YDR454C.1	IV:1366820-1366257	564	KGUA_YEAST	1-187	187	2	A:1-186 B:201-386	186 186

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
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Chain A from PDB  Type:PROTEIN  Length:186
 aligned with KGUA_YEAST | P15454 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
           KGUA_YEAST     2 SRPIVISGPSGTGKSTLLKKLFAEYPDSFGFSVSSTTRTPRAGEVNGKDYNFVSVDEFKSMIKNNEFIEWAQFSGNYYGSTVASVKQVSKSGKTCILDIDMQGVKSVKAIPELNARFLFIAPPSVEDLKKRLEGRGTETEESINKRLSAAQAELAYAETGAHDKVIVNDDLDKAYKELKDFIFAEK 187
               SCOP domains d1ex6a_ A: Guanylate kinase                                                                                                                                                                SCOP domains
               CATH domains 1ex6A02 A:1-32,A:93-186         1ex6A01 A:33-92 Guanylate Kinase phosphate binding domain   1ex6A02 A:1-32,A:93-186 P-loop containing nucleotide triphosphate hydrolases                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhh...ee....ee..............ee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhhh..eeeee.hhhhhhhhhh......eeeeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) GUANYLATE_KINASE_2  PDB: A:1-183 UniProt: 2-184                                                                                                                                        --- PROSITE (1)
                PROSITE (2) -----------------------------------GUANYLATE_KINASE_1------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:1-186 UniProt: 1-187 [INCOMPLETE]                                                                                                                                         Transcript 1
                 1ex6 A   1 SRPIVISGPSGTGKSTLLKKLFAEYPDSFGFSVSSTTRTPRAGEVNGKDYNFVSVDEFKSMIKNNEFIEWAQFSGNYYGSTVASVKQVSKSGKTCILDIDMQGVKSVKAIPELNARFLFIAPPSVEDLKKRLEGRGTETEESINKRLSAAQAELAYAETGAHDKVIVNDDLDKAYKELKDFIFAEK 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with KGUA_YEAST | P15454 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
           KGUA_YEAST     2 SRPIVISGPSGTGKSTLLKKLFAEYPDSFGFSVSSTTRTPRAGEVNGKDYNFVSVDEFKSMIKNNEFIEWAQFSGNYYGSTVASVKQVSKSGKTCILDIDMQGVKSVKAIPELNARFLFIAPPSVEDLKKRLEGRGTETEESINKRLSAAQAELAYAETGAHDKVIVNDDLDKAYKELKDFIFAEK 187
               SCOP domains d1ex6b_ B: Guanylate kinase                                                                                                                                                                SCOP domains
               CATH domains 1ex6B02 B:201-232,B:293-386     1ex6B01 B:233-292 Guanylate Kinase phosphate binding domain 1ex6B02 B:201-232,B:293-386 P-loop containing nucleotide triphosphate hydrolases               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhh...ee....ee..............ee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhhh..eeeee.hhhhhhhhhh......eeeeee..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) GUANYLATE_KINASE_2  PDB: B:201-383 UniProt: 2-184                                                                                                                                      --- PROSITE (1)
                PROSITE (2) -----------------------------------GUANYLATE_KINASE_1------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:201-386 UniProt: 1-187 [INCOMPLETE]                                                                                                                                       Transcript 1
                 1ex6 B 201 SRPIVISGPSGTGKSTLLKKLFAEYPDSFGFSVSSTTRTPRAGEVNGKDYNFVSVDEFKSMIKNNEFIEWAQFSGNYYGSTVASVKQVSKSGKTCILDIDMQGVKSVKAIPELNARFLFIAPPSVEDLKKRLEGRGTETEESINKRLSAAQAELAYAETGAHDKVIVNDDLDKAYKELKDFIFAEK 386
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

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)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d1ex6a_	A:
1b	d1ex6b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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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)

Baker's yeast (Saccharomyces cerevisiae) (3)

1a	1ex6A01	A:33-92
1b	1ex6B01	B:233-292

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

Topology: Rossmann fold (7312)

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

Baker's yeast (Saccharomyces cerevisiae) (61)

2a	1ex6A02	A:1-32,A:93-186
2b	1ex6B02	B:201-232,B:293-386

(no "Pfam Domain" information available for 1EX6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KGUA_YEAST | P15454)

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:0046711	GDP biosynthetic process	The chemical reactions and pathways resulting in the formation of 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.

Asymmetric/Biological Unit
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	1ex6
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	KGUA_YEAST \| P15454
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	2.7.4.8
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	KGUA_YEAST \| P15454
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UniProtKB/Swiss-Prot
	KGUA_YEAST \| P15454	:	1ex7 1gky 4f4j

1ex7	1EX7 IS THE CRYSTAL STRUCTURE OF A COMPLEX OF NON-(N- ACETYLATED) GUANYLATE KINASE FROM YEAST WITH GMP
1gky	1GKY IS THE CRYSTAL STRUCTURE OF A COMPLEX OF N-ACETYLATED GUANYLATE KINASE FROM YEAST WITH GMP

Description

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Ligands, Modified Residues, Ions (0, 0)

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PROSITE Motifs (2, 4)

Exons (1, 2)

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Gene Ontology (9, 9)

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