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Title :   CRYSTAL STRUCTURE OF GLUCONATE KINASE

Authors :   L. Kraft, G. A. Sprenger, Y. Lindqvist

Date :   20 Dec 01 (Deposition) - 29 May 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Alfa/Beta, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Kraft, G. A. Sprenger, Y. Lindqvist
Conformational Changes During The Catalytic Cycle Of Gluconate Kinase As Revealed By X-Ray Crystallography.
J. Mol. Biol. V. 318 1057 2002
PubMed-ID: 12054802 | Reference-DOI: 10.1016/S0022-2836(02)00215-2
(for further references see the PDB file header)

Molecule 1 - GLUCONATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PJF119EH
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GNTK
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	THERMORESISTANT GLUCONOKINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ACP	2	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:22 , ACP A:500 , HOH A:1023	BINDING SITE FOR RESIDUE MG A 1001
2	AC2	SOFTWARE	SER B:22 , ACP B:501	BINDING SITE FOR RESIDUE MG B 1002
3	AC3	SOFTWARE	VAL A:16 , SER A:17 , GLY A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , ALA A:23 , ARG A:120 , GLN A:158 , PRO A:159 , LEU A:160 , VAL A:163 , MG A:1001	BINDING SITE FOR RESIDUE ACP A 500
4	AC4	SOFTWARE	SER B:17 , GLY B:18 , GLY B:20 , LYS B:21 , SER B:22 , ALA B:23 , ARG B:120 , ARG B:124 , GLN B:158 , PRO B:159 , LEU B:160 , VAL B:163 , MG B:1002	BINDING SITE FOR RESIDUE ACP B 501

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

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

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

(no "PROSITE Motif" information available for 1KOF)

(no "Exon" information available for 1KOF)

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:171
 aligned with GNTK_ECOLI | P46859 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 
           GNTK_ECOLI     3 TTNHDHHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDFLHPRRNIEKMASGEPLNDDDRKPWLQALNDAAFAMQRTNKVSLIVCSALKKHYRDLLREGNPNLSFIYLKGDFDVIESRLKARKGHFFKTQMLVTQFETLQEPGADETDVLVVDIDQPLEGVVASTIEVIKK 173
               SCOP domains d1kofa_ A: Gluconate kinase                                                                                                                                                 SCOP domains
               CATH domains 1kofA00 A:3-173 P-loop containing nucleotide triphosphate hydrolases                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh....eeeeeee.hhhhhhhhhhhh.....hhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kof A   3 TTNHDHHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDFLHPRRNIEKMASGEPLNDDDRKPWLQALNDAAFAMQRTNKVSLIVCSALKKHYRDLLREGNPNLSFIYLKGDFDVIESRLKARKGHFFKTQMLVTQFETLQEPGADETDVLVVDIDQPLEGVVASTIEVIKK 173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with GNTK_ECOLI | P46859 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 
           GNTK_ECOLI     3 TTNHDHHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDFLHPRRNIEKMASGEPLNDDDRKPWLQALNDAAFAMQRTNKVSLIVCSALKKHYRDLLREGNPNLSFIYLKGDFDVIESRLKARKGHFFKTQMLVTQFETLQEPGADETDVLVVDIDQPLEGVVASTIEVIKK 173
               SCOP domains d1kofb_ B: Gluconate kinase                                                                                                                                                 SCOP domains
               CATH domains 1kofB00 B:3-173 P-loop containing nucleotide triphosphate hydrolases                                                                                                        CATH domains
           Pfam domains (1) --------------SKI-1kofB01 B:17-172                                                                                                                                        - Pfam domains (1)
           Pfam domains (2) --------------SKI-1kofB02 B:17-172                                                                                                                                        - Pfam domains (2)
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh....eeeeeee.hhhhhhhhhhh......hhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kof B   3 TTNHDHHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDFLHPRRNIEKMASGEPLNDDDRKPWLQALNDAAFAMQRTNKVSLIVCSALKKHYRDLLREGNPNLSFIYLKGDFDVIESRLKARKGHFFKTQMLVTQFETLQEPGADETDVLVVDIDQPLEGVVASTIEVIKK 173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

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: Gluconate kinase (6)

Protein domain: Gluconate kinase (6)

Escherichia coli [TaxId: 562] (6)

1a	d1kofa_	A:
1b	d1kofb_	B:

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)

Escherichia coli. Organism_taxid: 562. (54)

1a	1kofA00	A:3-173
1b	1kofB00	B:3-173

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: SKI (16)

Escherichia coli (strain K12) (6)

1a	SKI-1kofB01	B:17-172
1b	SKI-1kofB02	B:17-172

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GNTK_ECOLI | P46859)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046316	gluconokinase activity	Catalysis of the reaction: D-gluconate + ATP = 6-phospho-D-gluconate + ADP + 2 H(+).
	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:0046177	D-gluconate catabolic process	The chemical reactions and pathways resulting in the breakdown of D-gluconate, the anion of D-gluconic acid, the aldonic acid derived from glucose.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	1kof
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	2.7.1.12
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UniProtKB/Swiss-Prot
	GNTK_ECOLI \| P46859	:	1knq 1ko1 1ko4 1ko5 1ko8

1knq	1KNQ CONTAINS THE SAME PROTEIN, SPACE GROUP P212121.
1ko1	1KO1 CONTAINS THE SAME PROTEIN, SPACE GROUP C2.
1ko4	1KO4 CONTAINS THE SAME PROTEIN, SPACE GROUP P21212.
1ko5	1KO5 CONTAINS THE SAME PROTEIN COMPLEXED WITH ATP.
1ko8	1KO8 CONTAINS THE SAME PROTEIN COMPLEXED WITH GLUCONATE-6- PHOSPHATE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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Pfam Domains (1, 2)

Gene Ontology (8, 8)

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