EzCatDB: S00534
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DB codeS00534
CATH domainDomain 13.40.1190.20 : UDP-N-acetylmuramoyl-L-alanineCatalytic domain
E.C.2.7.1.15
CSA1rk2

CATH domainRelated DB codes (homologues)
3.40.1190.20 : UDP-N-acetylmuramoyl-L-alanineS00541,S00678,S00705,S00903,S00904,S00905,S00453,D00416

Enzyme Name
UniProtKBKEGG

P0A9J6
Protein nameRibokinaseribokinase
deoxyribokinase
ribokinase (phosphorylating)
D-ribokinase
SynonymsEC 2.7.1.15
RefSeqNP_418208.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491677.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF00294 (PfkB)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00030Pentose phosphate pathway

UniProtKB:Accession NumberP0A9J6
Entry nameRBSK_ECOLI
ActivityATP + D-ribose = ADP + D-ribose 5-phosphate.
SubunitHomodimer.
Subcellular locationCytoplasm.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00238C00009C00002C00121C01801C00008C00117C00673
CompoundMagnesiumPotassiumOrthophosphateATPD-Ribose2-Deoxy-D-riboseADPD-Ribose 5-phosphate2-Deoxy-D-ribose 5-phosphate
Typedivalent metal (Ca2+, Mg2+)univalent metal (Na+, K+)phosphate group/phosphate ionamine group,nucleotidecarbohydratecarbohydrateamine group,nucleotidecarbohydrate,phosphate group/phosphate ioncarbohydrate,phosphate group/phosphate ion
ChEBI18420
29103
26078
15422
47013

16761
52742
55513
PubChem888
813
22486802
1004
5957
5779
9828112
6022
439167
439288
                 
1gqtAUnboundAnalogue:_CSUnboundAnalogue:ACPBound:RIBUnboundUnboundUnboundUnbound
1gqtBUnboundAnalogue:_CSUnboundAnalogue:ACPBound:RIBUnboundUnboundUnboundUnbound
1gqtCUnboundAnalogue:_CSUnboundAnalogue:ACPBound:RIBUnboundUnboundUnboundUnbound
1gqtDUnboundAnalogue:_CSUnboundUnboundBound:RIBUnboundUnboundUnboundUnbound
1rk2AUnboundAnalogue:_MGUnboundUnboundBound:RIBUnboundBound:ADPUnboundUnbound
1rk2BUnboundAnalogue:_MGUnboundUnboundBound:RIBUnboundBound:ADPUnboundUnbound
1rk2CUnboundAnalogue:_MGUnboundUnboundBound:RIBUnboundBound:ADPUnboundUnbound
1rk2DUnboundAnalogue:_MGUnboundUnboundBound:RIBUnboundBound:ADPUnboundUnbound
1rkaAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1rkdAUnboundUnboundBound:PO4UnboundBound:RIBUnboundBound:ADPUnboundUnbound
1rksAUnboundUnboundBound:PO4UnboundBound:RIBUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [2], [3], [6], [8], [9], [13], [24]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
           
1gqtALYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1gqtBLYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1gqtCLYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1gqtDLYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1rk2ALYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1rk2BLYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1rk2CLYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1rk2DLYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1rkaALYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1rkdALYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254
1rksALYS 43;ASP 255
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)
ALA 252;ALA 253;GLY 254

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
CommentsCHARACTERIZATION.
PubMed ID9385653
JournalProtein Sci
Year1997
Volume6
Pages2474-6
AuthorsSigrell JA, Cameron AD, Jones TA, Mowbray SL
TitlePurification, characterization, and crystallization of Escherichia coli ribokinase.
Related UniProtKBP0A9J6
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF SHORT ISOFORM
Medline ID99060037
PubMed ID9843365
JournalBiochemistry
Year1998
Volume37
Pages15607-20
AuthorsMathews II, Erion MD, Ealick SE
TitleStructure of human adenosine kinase at 1.5 A resolution.
Related PDB1bx4
Related UniProtKBP55263
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS).
Medline ID98179935
PubMed ID9519409
JournalStructure
Year1998
Volume6
Pages183-93
AuthorsSigrell JA, Cameron AD, Jones TA, Mowbray SL
TitleStructure 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 PDB1rkd
Related UniProtKBP0A9J6
[4]
PubMed ID10393297
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages1309-19
AuthorsMowbray SL, Helgstrand C, Sigrell JA, Cameron AD, Jones TA
TitleErrors and reproducibility in electron-density map interpretation.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).
Medline ID99370056
PubMed ID10438599
JournalJ Mol Biol
Year1999
Volume290
Pages1009-18
AuthorsSigrell JA, Cameron AD, Mowbray SL
TitleInduced fit on sugar binding activates ribokinase.
Related PDB1rk2,1rka,1rks
Related UniProtKBP0A9J6
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, HOMOTRIMERIZATION, AND MUTAGENESIS OF CYS-198.
PubMed ID10891066
JournalBiochemistry
Year2000
Volume39
Pages7868-77
AuthorsCampobasso N, Mathews II, Begley TP, Ealick SE
TitleCrystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.
Related PDB1c3q,1esq,1esj,1ekq,1ekk
Related UniProtKBP39593
[7]
PubMed ID10648508
JournalJ Bacteriol
Year2000
Volume182
Pages869-73
AuthorsTourneux 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
TitleGenetic and biochemical characterization of Salmonella enterica serovar typhi deoxyribokinase.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS).
PubMed ID10801355
JournalJ Mol Biol
Year2000
Volume298
Pages875-93
AuthorsSchumacher MA, Scott DM, Mathews II, Ealick SE, Roos DS, Ullman B, Brennan RG
TitleCrystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding.
Related PDB1lii,1lij,1lik,1lio
Related UniProtKBQ9TVW2
[9]
PubMed ID11563694
JournalJ Protein Chem
Year2001
Volume20
Pages139-44
AuthorsMaj MC, Gupta RS
TitleThe effect of inorganic phosphate on the activity of bacterial ribokinase.
[10]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH ADP, AND SUBUNIT.
PubMed ID11286887
JournalStructure
Year2001
Volume9
Pages205-14
AuthorsIto S, Fushinobu S, Yoshioka I, Koga S, Matsuzawa H, Wakagi T
TitleStructural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon.
Related PDB1gc5
Related UniProtKBQ7M537
[11]
PubMed ID11900549
JournalBiochemistry
Year2002
Volume41
Pages4059-69
AuthorsMaj MC, Singh B, Gupta RS
TitlePentavalent 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.
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE; ADP AND COFACTOR.
PubMed ID12235162
JournalJ Biol Chem
Year2002
Volume277
Pages46385-90
AuthorsLi MH, Kwok F, Chang WR, Lau CK, Zhang JP, Lo SC, Jiang T, Liang DC
TitleCrystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.
Related PDB1lhp,1lhr
Related UniProtKBP82197
[13]
CommentsX-ray crystallography
PubMed ID11786021
JournalJ Mol Biol
Year2002
Volume315
Pages409-19
AuthorsAndersson CE, Mowbray SL
TitleActivation of ribokinase by monovalent cations.
Related PDB1gqt
[14]
CommentsX-ray crystallography
PubMed ID12457846
JournalJ Struct Biol
Year2002
Volume139
Pages161-70
AuthorsZhang RG, Grembecka J, Vinokour E, Collart F, Dementieva I, Minor W, Joachimiak A
TitleStructure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.
Related PDB1kyh
[15]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 23-266.
PubMed ID11839308
JournalStructure
Year2002
Volume10
Pages225-35
AuthorsCheng G, Bennett EM, Begley TP, Ealick SE
TitleCrystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution.
Related PDB1jxh,1jxi
Related UniProtKBP55882
[16]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH AMP AND GLUCOSE, AND SUBUNIT.
PubMed ID12909015
JournalJ Mol Biol
Year2003
Volume331
Pages871-83
AuthorsIto S, Fushinobu S, Jeong JJ, Yoshioka I, Koga S, Shoun H, Wakagi T
TitleCrystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase.
Related PDB1ua4
Related UniProtKBQ9V2Z6
[17]
Comments(ISSN 1442-0067)
JournalInternational Journal of Molecular Sciences
Year2004
Volume5
Pages141-53
AuthorsDyguda E, Szefczyk B, Sokalski WA
TitleThe mechanism of phosphoryl transfer reaction and the role of active site residues on the basis of ribokinase-like kinases.
[18]
PubMed ID15547280
JournalJ Bacteriol
Year2004
Volume186
Pages8074-82
AuthorsSafo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V
TitleCrystal structure of the PdxY Protein from Escherichia coli.
Related PDB1td2
Related UniProtKBP77150
[19]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
PubMed ID15210349
JournalJ Mol Biol
Year2004
Volume340
Pages477-89
AuthorsOhshima N, Inagaki E, Yasuike K, Takio K, Tahirov TH
TitleStructure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.
Related PDB1v19,1v1a,1v1b,1v1s
Related UniProtKBQ746L7
[20]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
PubMed ID15458630
JournalStructure
Year2004
Volume12
Pages1809-21
AuthorsZhang Y, Dougherty M, Downs DM, Ealick SE
TitleCrystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.
Related PDB1tyy,1tz3,1tz6
Related UniProtKBQ8ZKR2
[21]
PubMed ID16030223
JournalJ Bacteriol
Year2005
Volume187
Pages5292-300
AuthorsMcArthur F, Andersson CE, Loutet S, Mowbray SL, Valvano MA
TitleFunctional 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.
[22]
CommentsX-ray crystallography
PubMed ID16929110
JournalActa Crystallogr D Biol Crystallogr
Year2006
Volume62
Pages1085-97
AuthorsArnfors L, Hansen T, Schonheit P, Ladenstein R, Meining W
TitleStructure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.
Related PDB2c4e,2c49
[23]
PubMed ID16866375
JournalBiochemistry
Year2006
Volume45
Pages9291-9
AuthorsParducci RE, Cabrera R, Baez M, Guixe V
TitleEvidence for a catalytic Mg2+ ion and effect of phosphate on the activity of Escherichia coli phosphofructokinase-2: regulatory properties of a ribokinase family member.
[24]
PubMed ID16784868
JournalBioorg Med Chem
Year2006
Volume14
Pages6327-32
AuthorsChuvikovsky DV, Esipov RS, Skoblov YS, Chupova LA, Muravyova TI, Miroshnikov AI, Lapinjoki S, Mikhailopulo IA
TitleRibokinase from E. coli: expression, purification, and substrate specificity.
[25]
PubMed ID16740960
JournalJ Bacteriol
Year2006
Volume188
Pages4542-52
AuthorsSafo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V
TitleCrystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
Related PDB2ddm,2ddo,2ddw
[26]
CommentsX-ray crystallography
PubMed ID16978644
JournalJ Mol Biol
Year2006
Volume363
Pages520-30
AuthorsNewman JA, Das SK, Sedelnikova SE, Rice DW
TitleThe crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.
Related PDB2i5b

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 human counterpart enzyme (S00541 in EzCatDB).

createdupdated
2007-03-012009-03-19


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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