S00534
type: Enzyme
cath: UDP-N-acetylmuramoyl-L-alanine
ec: https://purl.uniprot.org/enzyme/2.7.1.15
csa: 1rk2
uniprot: P0A9J6
kegg enzyme: ribokinase
kegg enzyme: deoxyribokinase
kegg enzyme: ribokinase (phosphorylating)
kegg enzyme: D-ribokinase
kegg pathway: Pentose phosphate pathway
kegg cofactor: Magnesium
kegg cofactor: Potassium
kegg cofactor: Orthophosphate
kegg substrate: ATP
kegg substrate: D-Ribose
kegg substrate: 2-Deoxy-D-ribose
kegg product: ADP
kegg product: D-Ribose 5-phosphate
kegg product: 2-Deoxy-D-ribose 5-phosphate
pdb: 1gqtA
pdb: 1gqtB
pdb: 1gqtC
pdb: 1gqtD
pdb: 1rk2A
pdb: 1rk2B
pdb: 1rk2C
pdb: 1rk2D
pdb: 1rkaA
pdb: 1rkdA
pdb: 1rksA
pdb bound state: Analogue
  compound: ATP
  pdb: 1gqtA
  ligand het code: ACP
pdb bound state: Analogue
  compound: ATP
  pdb: 1gqtB
  ligand het code: ACP
pdb bound state: Analogue
  compound: ATP
  pdb: 1gqtC
  ligand het code: ACP
pdb bound state: Unbound
  compound: ATP
  pdb: 1gqtD
pdb bound state: Unbound
  compound: ATP
  pdb: 1rk2A
pdb bound state: Unbound
  compound: ATP
  pdb: 1rk2B
pdb bound state: Unbound
  compound: ATP
  pdb: 1rk2C
pdb bound state: Unbound
  compound: ATP
  pdb: 1rk2D
pdb bound state: Unbound
  compound: ATP
  pdb: 1rkaA
pdb bound state: Unbound
  compound: ATP
  pdb: 1rkdA
pdb bound state: Unbound
  compound: ATP
  pdb: 1rksA
pdb bound state: Unbound
  compound: D-Ribose
  pdb: 1rkaA
pdb bound state: Unbound
  compound: 2-Deoxy-D-ribose
  pdb: 1gqtA
pdb bound state: Unbound
  compound: 2-Deoxy-D-ribose
  pdb: 1gqtB
pdb bound state: Unbound
  compound: 2-Deoxy-D-ribose
  pdb: 1gqtC
pdb bound state: Unbound
  compound: 2-Deoxy-D-ribose
  pdb: 1gqtD
active site residues resources: Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures.
active site residues resources: Errors and reproducibility in electron-density map interpretation.
active site residues resources: Genetic and biochemical characterization of Salmonella enterica serovar typhi deoxyribokinase.
active site residues resources: The effect of inorganic phosphate on the activity of bacterial ribokinase.
active site residues resources: Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon.
active site residues resources: Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.
active site residues resources: Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
references: Purification, characterization, and crystallization of Escherichia coli ribokinase.
references: Structure of human adenosine kinase at 1.5 A resolution.
references: Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures.
references: Errors and reproducibility in electron-density map interpretation.
references: Induced fit on sugar binding activates ribokinase.
references: Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.
references: Genetic and biochemical characterization of Salmonella enterica serovar typhi deoxyribokinase.
references: Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding.
references: The effect of inorganic phosphate on the activity of bacterial ribokinase.
references: Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon.
references: http://ezcatdb.cbrc.jp/EzCatDB/reference/S00534#11
references: Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.
references: Activation of ribokinase by monovalent cations.
references: Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.
references: Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution.
references: Crystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase.
references: The mechanism of phosphoryl transfer reaction and the role of active site residues on the basis of ribokinase-like kinases.
references: Crystal structure of the PdxY Protein from Escherichia coli.
references: Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.
references: Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.
references: Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis.
references: Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.
references: Evidence for a catalytic Mg2+ ion and effect of phosphate on the activity of Escherichia coli phosphofructokinase-2: regulatory properties of a ribokinase family member.
references: Ribokinase from E. coli: expression, purification, and substrate specificity.
references: Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
references: The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.
comment: Althogh potassium ion and phosphate ion are included as cofactors, they are not likely to be involved in catalysis (see [9], [13], [24]). This enzyme is homologous to human counterpart enzyme (S00541 in EzCatDB).

UDP-N-acetylmuramoyl-L-alanine
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.1190.20
catalytic domain: index.html

Pentose phosphate pathway
type: KeggPathway
references: KEGG:MAP00030

Magnesium
type: KeggCofactor
references: KEGG:C00305
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:18420
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Potassium
type: KeggCofactor
references: KEGG:C00238
compound type: univalent metal (Na+, K+)
references: CHEBI:29103
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Orthophosphate
type: KeggCofactor
references: KEGG:C00009
compound type: phosphate group/phosphate ion
references: CHEBI:26078
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

ATP
type: KeggSubstrate
references: KEGG:C00002
compound type: amine group
compound type: nucleotide
references: CHEBI:15422
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

D-Ribose
type: KeggSubstrate
references: KEGG:C00121
compound type: carbohydrate
references: CHEBI:47013
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

2-Deoxy-D-ribose
type: KeggSubstrate
references: KEGG:C01801
compound type: carbohydrate
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

ADP
type: KeggProduct
references: KEGG:C00008
compound type: amine group
compound type: nucleotide
references: CHEBI:16761
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

D-Ribose 5-phosphate
type: KeggProduct
references: KEGG:C00117
compound type: carbohydrate
compound type: phosphate group/phosphate ion
references: CHEBI:52742
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

2-Deoxy-D-ribose 5-phosphate
type: KeggProduct
references: KEGG:C00673
compound type: carbohydrate
compound type: phosphate group/phosphate ion
references: CHEBI:55513
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1gqtA
type: Pdb
references: 1gqt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1gqt
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1gqtB
type: Pdb
references: 1gqt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1gqt
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1gqtC
type: Pdb
references: 1gqt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1gqt
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1gqtD
type: Pdb
references: 1gqt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1gqt
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1rk2A
type: Pdb
references: 1rk2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1rk2
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1rk2B
type: Pdb
references: 1rk2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1rk2
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1rk2C
type: Pdb
references: 1rk2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1rk2
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1rk2D
type: Pdb
references: 1rk2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1rk2
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1rkaA
type: Pdb
references: 1rka
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1rka
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1rkdA
type: Pdb
references: 1rkd
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1rkd
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

1rksA
type: Pdb
references: 1rks
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1rks
catalytic residue: LYS 43;ASP 255
cofactor binding residue: THR 250(magnesium-1 binding);ASN 166;ASN 187;GLU 190(magnesium-2 binding);ASP 249;ILE 251;ALA 285;ARG 288;GLY 290;SER 294(potassium binding);ALA 170;ASN 187(orthophosphate binding)
main chain in catalysis: ALA 252;ALA 253;GLY 254

Purification, characterization, and crystallization of Escherichia coli ribokinase.
type: BibliographicResource
comment: CHARACTERIZATION.
references: http://www.ncbi.nlm.nih.gov/pubmed/9385653
journal: Protein Sci
volume: 6
pages: 2474-6
published year: 1997
authors:
  item: Sigrell JA
  item: Cameron AD
  item: Jones TA
  item: Mowbray SL
references: P0A9J6

Structure of human adenosine kinase at 1.5 A resolution.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF SHORT ISOFORM
medline id: 99060037
references: http://www.ncbi.nlm.nih.gov/pubmed/9843365
journal: Biochemistry
volume: 37
pages: 15607-20
published year: 1998
authors:
  item: Mathews II
  item: Erion MD
  item: Ealick SE
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P55263

Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS).
medline id: 98179935
references: http://www.ncbi.nlm.nih.gov/pubmed/9519409
journal: Structure
volume: 6
pages: 183-93
published year: 1998
authors:
  item: Sigrell JA
  item: Cameron AD
  item: Jones TA
  item: Mowbray SL
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P0A9J6

Errors and reproducibility in electron-density map interpretation.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10393297
journal: Acta Crystallogr D Biol Crystallogr
volume: 55
pages: 1309-19
published year: 1999
authors:
  item: Mowbray SL
  item: Helgstrand C
  item: Sigrell JA
  item: Cameron AD
  item: Jones TA

Induced fit on sugar binding activates ribokinase.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).
medline id: 99370056
references: http://www.ncbi.nlm.nih.gov/pubmed/10438599
journal: J Mol Biol
volume: 290
pages: 1009-18
published year: 1999
authors:
  item: Sigrell JA
  item: Cameron AD
  item: Mowbray SL
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P0A9J6

Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, HOMOTRIMERIZATION, AND MUTAGENESIS OF CYS-198.
references: http://www.ncbi.nlm.nih.gov/pubmed/10891066
journal: Biochemistry
volume: 39
pages: 7868-77
published year: 2000
authors:
  item: Campobasso N
  item: Mathews II
  item: Begley TP
  item: Ealick SE
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P39593

Genetic and biochemical characterization of Salmonella enterica serovar typhi deoxyribokinase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10648508
journal: J Bacteriol
volume: 182
pages: 869-73
published year: 2000
authors:
  item: Tourneux L
  item: Bucurenci N
  item: Saveanu C
  item: Kaminski PA
  item: Bouzon M
  item: Pistotnik E
  item: Namane A
  item: Marliere P
  item: Barzu O
  item: De La Sierra IL
  item: Neuhard J
  item: Gilles AM

Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/10801355
journal: J Mol Biol
volume: 298
pages: 875-93
published year: 2000
authors:
  item: Schumacher MA
  item: Scott DM
  item: Mathews II
  item: Ealick SE
  item: Roos DS
  item: Ullman B
  item: Brennan RG
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q9TVW2

The effect of inorganic phosphate on the activity of bacterial ribokinase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11563694
journal: J Protein Chem
volume: 20
pages: 139-44
published year: 2001
authors:
  item: Maj MC
  item: Gupta RS

Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH ADP, AND SUBUNIT.
references: http://www.ncbi.nlm.nih.gov/pubmed/11286887
journal: Structure
volume: 9
pages: 205-14
published year: 2001
authors:
  item: Ito S
  item: Fushinobu S
  item: Yoshioka I
  item: Koga S
  item: Matsuzawa H
  item: Wakagi T
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q7M537

http://ezcatdb.cbrc.jp/EzCatDB/reference/S00534#11
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11900549
journal: Biochemistry
volume: 41
pages: 4059-69
published year: 2002
authors:
  item: Maj MC
  item: Singh B
  item: Gupta RS
title: Pentavalent ions dependency is a conserved property of adenosine kinase from diverse sources: identification of a novel motif implicated in phosphate and magnesium ion binding and substrate inhibition.

Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE; ADP AND COFACTOR.
references: http://www.ncbi.nlm.nih.gov/pubmed/12235162
journal: J Biol Chem
volume: 277
pages: 46385-90
published year: 2002
authors:
  item: Li MH
  item: Kwok F
  item: Chang WR
  item: Lau CK
  item: Zhang JP
  item: Lo SC
  item: Jiang T
  item: Liang DC
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P82197

Activation of ribokinase by monovalent cations.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/11786021
journal: J Mol Biol
volume: 315
pages: 409-19
published year: 2002
authors:
  item: Andersson CE
  item: Mowbray SL
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/12457846
journal: J Struct Biol
volume: 139
pages: 161-70
published year: 2002
authors:
  item: Zhang RG
  item: Grembecka J
  item: Vinokour E
  item: Collart F
  item: Dementieva I
  item: Minor W
  item: Joachimiak A
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 23-266.
references: http://www.ncbi.nlm.nih.gov/pubmed/11839308
journal: Structure
volume: 10
pages: 225-35
published year: 2002
authors:
  item: Cheng G
  item: Bennett EM
  item: Begley TP
  item: Ealick SE
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P55882

Crystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH AMP AND GLUCOSE, AND SUBUNIT.
references: http://www.ncbi.nlm.nih.gov/pubmed/12909015
journal: J Mol Biol
volume: 331
pages: 871-83
published year: 2003
authors:
  item: Ito S
  item: Fushinobu S
  item: Jeong JJ
  item: Yoshioka I
  item: Koga S
  item: Shoun H
  item: Wakagi T
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q9V2Z6

The mechanism of phosphoryl transfer reaction and the role of active site residues on the basis of ribokinase-like kinases.
type: BibliographicResource
comment: (ISSN 1442-0067)
journal: International Journal of Molecular Sciences
volume: 5
pages: 141-53
published year: 2004
authors:
  item: Dyguda E
  item: Szefczyk B
  item: Sokalski WA

Crystal structure of the PdxY Protein from Escherichia coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/15547280
journal: J Bacteriol
volume: 186
pages: 8074-82
published year: 2004
authors:
  item: Safo MK
  item: Musayev FN
  item: Hunt S
  item: di Salvo ML
  item: Scarsdale N
  item: Schirch V
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P77150

Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/15210349
journal: J Mol Biol
volume: 340
pages: 477-89
published year: 2004
authors:
  item: Ohshima N
  item: Inagaki E
  item: Yasuike K
  item: Takio K
  item: Tahirov TH
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q746L7

Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/15458630
journal: Structure
volume: 12
pages: 1809-21
published year: 2004
authors:
  item: Zhang Y
  item: Dougherty M
  item: Downs DM
  item: Ealick SE
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q8ZKR2

Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/16030223
journal: J Bacteriol
volume: 187
pages: 5292-300
published year: 2005
authors:
  item: McArthur F
  item: Andersson CE
  item: Loutet S
  item: Mowbray SL
  item: Valvano MA

Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/16929110
journal: Acta Crystallogr D Biol Crystallogr
volume: 62
pages: 1085-97
published year: 2006
authors:
  item: Arnfors L
  item: Hansen T
  item: Schonheit P
  item: Ladenstein R
  item: Meining W
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Evidence for a catalytic Mg2+ ion and effect of phosphate on the activity of Escherichia coli phosphofructokinase-2: regulatory properties of a ribokinase family member.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/16866375
journal: Biochemistry
volume: 45
pages: 9291-9
published year: 2006
authors:
  item: Parducci RE
  item: Cabrera R
  item: Baez M
  item: Guixe V

Ribokinase from E. coli: expression, purification, and substrate specificity.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/16784868
journal: Bioorg Med Chem
volume: 14
pages: 6327-32
published year: 2006
authors:
  item: Chuvikovsky DV
  item: Esipov RS
  item: Skoblov YS
  item: Chupova LA
  item: Muravyova TI
  item: Miroshnikov AI
  item: Lapinjoki S
  item: Mikhailopulo IA

Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/16740960
journal: J Bacteriol
volume: 188
pages: 4542-52
published year: 2006
authors:
  item: Safo MK
  item: Musayev FN
  item: di Salvo ML
  item: Hunt S
  item: Claude JB
  item: Schirch V
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/16978644
journal: J Mol Biol
volume: 363
pages: 520-30
published year: 2006
authors:
  item: Newman JA
  item: Das SK
  item: Sedelnikova SE
  item: Rice DW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Analogue
compound: Potassium
pdb: 1gqtA
ligand het code: _CS

Analogue
compound: Potassium
pdb: 1gqtB
ligand het code: _CS

Analogue
compound: Potassium
pdb: 1gqtC
ligand het code: _CS

Analogue
compound: Potassium
pdb: 1gqtD
ligand het code: _CS

Analogue
compound: Potassium
pdb: 1rk2A
ligand het code: _MG

Analogue
compound: Potassium
pdb: 1rk2B
ligand het code: _MG

Analogue
compound: Potassium
pdb: 1rk2C
ligand het code: _MG

Analogue
compound: Potassium
pdb: 1rk2D
ligand het code: _MG

ReferenceForCatalyticMechanism
reference index: 2
reference section: p.15617-15618, Fig.12

ReferenceForCatalyticMechanism
reference index: 3
reference section: p.186, p.188-189

ReferenceForCatalyticMechanism
reference index: 5
reference section: p.1015-1016

ReferenceForCatalyticMechanism
reference index: 6
reference section: p.7876-7877

ReferenceForCatalyticMechanism
reference index: 8
reference section: p.886-890

ReferenceForCatalyticMechanism
reference index: 11
reference section: Fig.1, Fig.6

ReferenceForCatalyticMechanism
reference index: 13
reference section: p.410-412, p.415-417

ReferenceForCatalyticMechanism
reference index: 17
reference section: Fig.5, Fig.6, p.147-151

ReferenceForCatalyticMechanism
reference index: 20
reference section: p.1815-1819

ReferenceForCatalyticMechanism
reference index: 23
reference section: p.9296-9298

ReferenceForCatalyticMechanism
reference index: 25
reference section: p.4545-4547, p.4549

ReferenceForCatalyticMechanism
reference index: 26
reference section: p.525-528