EzCatDB: S00301
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DB codeS00301
RLCP classification3.103.70035.355 : Transfer
CATH domainDomain 13.40.50.300 : Rossmann foldCatalytic domain
E.C.2.7.1.19

CATH domainRelated DB codes (homologues)
3.40.50.300 : Rossmann foldS00527,S00547,S00548,S00550,S00554,S00555,S00671,S00672,S00676,S00680,S00682,S00913,S00914,S00302,S00303,S00304,S00307,S00308,S00305,S00306,S00309,S00310,S00311,M00114,M00199,D00129,D00130,D00540,M00186

Enzyme Name
UniProtKBKEGG

P12033
Protein namePhosphoribulokinase 1phosphoribulokinase
phosphopentokinase
ribulose-5-phosphate kinase
phosphopentokinase
phosphoribulokinase (phosphorylating)
5-phosphoribulose kinase
ribulose phosphate kinase
PKK
PRuK
PRK
SynonymsPRKase 1
PRK I
EC 2.7.1.19
Phosphopentokinase 1
PfamPF00485 (PRK)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00710Carbon fixation in photosynthetic organisms

UniProtKB:Accession NumberP12033
Entry nameKPPR1_RHOSH
ActivityATP + D-ribulose 5-phosphate = ADP + D- ribulose 1,5-bisphosphate.
SubunitHomooctamer.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00002C00199C00008C01182
CompoundmagnesiumATPD-Ribulose 5-phosphateADPD-Ribulose 1,5-bisphosphate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidecarbohydrate,phosphate group/phosphate ionamine group,nucleotidecarbohydrate,phosphate group/phosphate ion
ChEBI18420
15422
17363
16761
16710
PubChem888
5957
439184
6022
123658
             
1a7jAUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
PDB;1a7j & literature [4]
pdbCatalytic residuesCofactor-binding residues
          
1a7jAASP 42;HIS 45;ARG 49;LYS 165;ARG 168;ASP 169;ARG 173
GLU 131 (Mg2+ binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.113-124

references
[1]
PubMed ID9548738
JournalBiochemistry
Year1998
Volume37
Pages5074-85
AuthorsHarrison DH, Runquist JA, Holub A, Miziorko HM
TitleThe crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase.
[2]
PubMed ID9477947
JournalBiochemistry
Year1998
Volume37
Pages1221-6
AuthorsRunquist JA, Harrison DH, Miziorko HM
TitleFunctional evaluation of invariant arginines situated in the mobile lid domain of phosphoribulokinase.
[3]
PubMed ID10563798
JournalBiochemistry
Year1999
Volume38
Pages15157-65
AuthorsKung G, Runquist JA, Miziorko HM, Harrison DH
TitleIdentification of the allosteric regulatory site in bacterial phosphoribulokinase.
[4]
PubMed ID10800594
JournalAdv Enzymol Relat Areas Mol Biol
Year2000
Volume74
Pages95-127
AuthorsMiziorko HM
TitlePhosphoribulokinase: current perspectives on the structure/function basis for regulation and catalysis.

comments
This enzyme belongs to the phosphoribulokinase family.
According to the literature [4], Asp42 is considered to be a general base, which may deprotonate C1 hydroxy group of the substrate, ribulose-5-phosphate, and facilitate its nucleophilic attack on gamma-phosphoryl group of ATP. In contrast, Glu131 is postulated to anchor the gamma-phosphoryl group through divalent metal ligation.
There are several invariant basic residues (Arg49, Lys165), which might be involved in catalysis, although their functions have not been annotated [4]. These basic residues can guide the transfer of the phosphoryl group of ATP, by stabilizing it.

createdupdated
2002-05-312009-02-26


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