DB code: S00541

CATH domain 3.40.1190.20 : UDP-N-acetylmuramoyl-L-alanine Catalytic domain
E.C. 2.7.1.15
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.1190.20 : UDP-N-acetylmuramoyl-L-alanine S00534 S00678 S00705 S00903 S00904 S00905 S00453 D00416

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q9H477 Ribokinase
EC 2.7.1.15
NP_071411.1 (Protein)
NM_022128.1 (DNA/RNA sequence)
PF00294 (PfkB)
[Graphical View]

KEGG enzyme name
ribokinase
deoxyribokinase
ribokinase (phosphorylating)
D-ribokinase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q9H477 RBSK_HUMAN ATP + D-ribose = ADP + D-ribose 5-phosphate.

KEGG Pathways
Map code Pathways E.C.
MAP00030 Pentose phosphate pathway

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00238 C00009 C00002 C00121 C01801 C00008 C00117 C00673
E.C.
Compound Magnesium Potassium Orthophosphate ATP D-Ribose 2-Deoxy-D-ribose ADP D-Ribose 5-phosphate 2-Deoxy-D-ribose 5-phosphate
Type divalent metal (Ca2+, Mg2+) univalent metal (Na+, K+) phosphate group/phosphate ion amine group,nucleotide carbohydrate carbohydrate amine group,nucleotide carbohydrate,phosphate group/phosphate ion carbohydrate,phosphate group/phosphate ion
ChEBI 18420
29103
26078
15422
47013
16761
52742
55513
PubChem 888
813
1004
22486802
5957
5779
9828112
6022
439167
439288
2fv7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Bound:_NA Unbound Unbound Unbound Unbound Bound:ADP Unbound Unbound
2fv7B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Bound:_NA Unbound Unbound Unbound Unbound Bound:ADP Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2], [3], [6], [8], [13]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2fv7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 54;ASP 269 ASP 263;SER 301;ALA 304;SER 310(potassium);ALA 181;ASN 199(orthophosphate) GLY 266;ALA 267;GLY 268
2fv7B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 54;ASP 269 ASP 263;SER 301;ALA 304;SER 310(potassium);ALA 181;ASN 199(orthophosphate) GLY 266;ALA 267;GLY 268

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
p.15617-15618, Fig.12
[3]
p.186, p.188-189
[5]
p.1015-1016
[6]
p.7876-7877
[8]
p.886-890
[11]
Fig.1, Fig.6
[13]
p.410-412, p.415-417
[17]
Fig.5, Fig.6, p.147-151
[20]
p.1815-1819
[23]
p.9296-9298
[25]
p.4545-4547, p.4549
[26]
p.525-528

References
[1]
Resource
Comments CHARACTERIZATION.
Medline ID
PubMed ID 9385653
Journal Protein Sci
Year 1997
Volume 6
Pages 2474-6
Authors Sigrell JA, Cameron AD, Jones TA, Mowbray SL
Title Purification, characterization, and crystallization of Escherichia coli ribokinase.
Related PDB
Related UniProtKB P0A9J6
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF SHORT ISOFORM
Medline ID 99060037
PubMed ID 9843365
Journal Biochemistry
Year 1998
Volume 37
Pages 15607-20
Authors Mathews II, Erion MD, Ealick SE
Title Structure of human adenosine kinase at 1.5 A resolution.
Related PDB 1bx4
Related UniProtKB P55263
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS).
Medline ID 98179935
PubMed ID 9519409
Journal Structure
Year 1998
Volume 6
Pages 183-93
Authors Sigrell JA, Cameron AD, Jones TA, Mowbray SL
Title 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.
Related PDB 1rkd
Related UniProtKB P0A9J6
[4]
Resource
Comments
Medline ID
PubMed ID 10393297
Journal Acta Crystallogr D Biol Crystallogr
Year 1999
Volume 55
Pages 1309-19
Authors Mowbray SL, Helgstrand C, Sigrell JA, Cameron AD, Jones TA
Title Errors and reproducibility in electron-density map interpretation.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).
Medline ID 99370056
PubMed ID 10438599
Journal J Mol Biol
Year 1999
Volume 290
Pages 1009-18
Authors Sigrell JA, Cameron AD, Mowbray SL
Title Induced fit on sugar binding activates ribokinase.
Related PDB 1rk2 1rka 1rks
Related UniProtKB P0A9J6
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, HOMOTRIMERIZATION, AND MUTAGENESIS OF CYS-198.
Medline ID
PubMed ID 10891066
Journal Biochemistry
Year 2000
Volume 39
Pages 7868-77
Authors Campobasso N, Mathews II, Begley TP, Ealick SE
Title Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.
Related PDB 1c3q 1esq 1esj 1ekq 1ekk
Related UniProtKB P39593
[7]
Resource
Comments
Medline ID
PubMed ID 10648508
Journal J Bacteriol
Year 2000
Volume 182
Pages 869-73
Authors Tourneux L, Bucurenci N, Saveanu C, Kaminski PA, Bouzon M, Pistotnik E, Namane A, Marliere P, Barzu O, De La Sierra IL, Neuhard J, Gilles AM
Title Genetic and biochemical characterization of Salmonella enterica serovar typhi deoxyribokinase.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS).
Medline ID
PubMed ID 10801355
Journal J Mol Biol
Year 2000
Volume 298
Pages 875-93
Authors Schumacher MA, Scott DM, Mathews II, Ealick SE, Roos DS, Ullman B, Brennan RG
Title Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding.
Related PDB 1lii 1lij 1lik 1lio
Related UniProtKB Q9TVW2
[9]
Resource
Comments
Medline ID
PubMed ID 11563694
Journal J Protein Chem
Year 2001
Volume 20
Pages 139-44
Authors Maj MC, Gupta RS
Title The effect of inorganic phosphate on the activity of bacterial ribokinase.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH ADP, AND SUBUNIT.
Medline ID
PubMed ID 11286887
Journal Structure
Year 2001
Volume 9
Pages 205-14
Authors Ito S, Fushinobu S, Yoshioka I, Koga S, Matsuzawa H, Wakagi T
Title Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon.
Related PDB 1gc5
Related UniProtKB Q7M537
[11]
Resource
Comments
Medline ID
PubMed ID 11900549
Journal Biochemistry
Year 2002
Volume 41
Pages 4059-69
Authors Maj MC, Singh B, 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.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE; ADP AND COFACTOR.
Medline ID
PubMed ID 12235162
Journal J Biol Chem
Year 2002
Volume 277
Pages 46385-90
Authors Li MH, Kwok F, Chang WR, Lau CK, Zhang JP, Lo SC, Jiang T, Liang DC
Title Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.
Related PDB 1lhp 1lhr
Related UniProtKB P82197
[13]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11786021
Journal J Mol Biol
Year 2002
Volume 315
Pages 409-19
Authors Andersson CE, Mowbray SL
Title Activation of ribokinase by monovalent cations.
Related PDB 1gqt
Related UniProtKB
[14]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 12457846
Journal J Struct Biol
Year 2002
Volume 139
Pages 161-70
Authors Zhang RG, Grembecka J, Vinokour E, Collart F, Dementieva I, Minor W, Joachimiak A
Title Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.
Related PDB 1kyh
Related UniProtKB
[15]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 23-266.
Medline ID
PubMed ID 11839308
Journal Structure
Year 2002
Volume 10
Pages 225-35
Authors Cheng G, Bennett EM, Begley TP, Ealick SE
Title Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution.
Related PDB 1jxh 1jxi
Related UniProtKB P55882
[16]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH AMP AND GLUCOSE, AND SUBUNIT.
Medline ID
PubMed ID 12909015
Journal J Mol Biol
Year 2003
Volume 331
Pages 871-83
Authors Ito S, Fushinobu S, Jeong JJ, Yoshioka I, Koga S, Shoun H, Wakagi T
Title Crystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase.
Related PDB 1ua4
Related UniProtKB Q9V2Z6
[17]
Resource
Comments (ISSN 1442-0067)
Medline ID
PubMed ID
Journal International Journal of Molecular Sciences
Year 2004
Volume 5
Pages 141-53
Authors Dyguda E, Szefczyk B, Sokalski WA
Title The mechanism of phosphoryl transfer reaction and the role of active site residues on the basis of ribokinase-like kinases.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 15547280
Journal J Bacteriol
Year 2004
Volume 186
Pages 8074-82
Authors Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V
Title Crystal structure of the PdxY Protein from Escherichia coli.
Related PDB 1td2
Related UniProtKB P77150
[19]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID
PubMed ID 15210349
Journal J Mol Biol
Year 2004
Volume 340
Pages 477-89
Authors Ohshima N, Inagaki E, Yasuike K, Takio K, Tahirov TH
Title Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.
Related PDB 1v19 1v1a 1v1b 1v1s
Related UniProtKB Q746L7
[20]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
Medline ID
PubMed ID 15458630
Journal Structure
Year 2004
Volume 12
Pages 1809-21
Authors Zhang Y, Dougherty M, Downs DM, Ealick SE
Title Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.
Related PDB 1tyy 1tz3 1tz6
Related UniProtKB Q8ZKR2
[21]
Resource
Comments
Medline ID
PubMed ID 16030223
Journal J Bacteriol
Year 2005
Volume 187
Pages 5292-300
Authors McArthur F, Andersson CE, Loutet S, Mowbray SL, Valvano MA
Title 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.
Related PDB
Related UniProtKB
[22]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 16929110
Journal Acta Crystallogr D Biol Crystallogr
Year 2006
Volume 62
Pages 1085-97
Authors Arnfors L, Hansen T, Schonheit P, Ladenstein R, Meining W
Title Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.
Related PDB 2c4e 2c49
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 16866375
Journal Biochemistry
Year 2006
Volume 45
Pages 9291-9
Authors Parducci RE, Cabrera R, Baez M, Guixe V
Title 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.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 16784868
Journal Bioorg Med Chem
Year 2006
Volume 14
Pages 6327-32
Authors Chuvikovsky DV, Esipov RS, Skoblov YS, Chupova LA, Muravyova TI, Miroshnikov AI, Lapinjoki S, Mikhailopulo IA
Title Ribokinase from E. coli: expression, purification, and substrate specificity.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 16740960
Journal J Bacteriol
Year 2006
Volume 188
Pages 4542-52
Authors Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V
Title Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
Related PDB 2ddm 2ddo 2ddw
Related UniProtKB
[26]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 16978644
Journal J Mol Biol
Year 2006
Volume 363
Pages 520-30
Authors Newman JA, Das SK, Sedelnikova SE, Rice DW
Title The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.
Related PDB 2i5b
Related UniProtKB

Comments
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 bacterial counterpart enzyme (S00534 in EzCatDB).

Created Updated
2007-03-01 2009-03-19