DB code: S00301

RLCP classification 3.103.70035.355 : Transfer
CATH domain 3.40.50.300 : Rossmann fold Catalytic domain
E.C. 2.7.1.19
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.300 : Rossmann fold S00527 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P12033 Phosphoribulokinase 1
PRKase 1
PRK I
EC 2.7.1.19
Phosphopentokinase 1
PF00485 (PRK)
[Graphical View]

KEGG enzyme name
phosphoribulokinase
phosphopentokinase
ribulose-5-phosphate kinase
phosphopentokinase
phosphoribulokinase (phosphorylating)
5-phosphoribulose kinase
ribulose phosphate kinase
PKK
PRuK
PRK

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P12033 KPPR1_RHOSH ATP + D-ribulose 5-phosphate = ADP + D- ribulose 1,5-bisphosphate. Homooctamer.

KEGG Pathways
Map code Pathways E.C.
MAP00710 Carbon fixation in photosynthetic organisms

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00199 C00008 C01182
E.C.
Compound magnesium ATP D-Ribulose 5-phosphate ADP D-Ribulose 1,5-bisphosphate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide carbohydrate,phosphate group/phosphate ion amine group,nucleotide carbohydrate,phosphate group/phosphate ion
ChEBI 18420
15422
17363
16761
16710
PubChem 888
5957
439184
6022
123658
1a7jA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1a7j & literature [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1a7jA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 42;HIS 45;ARG 49;LYS 165;ARG 168;ASP 169;ARG 173 GLU 131 (Mg2+ binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.113-124

References
[1]
Resource
Comments
Medline ID
PubMed ID 9548738
Journal Biochemistry
Year 1998
Volume 37
Pages 5074-85
Authors Harrison DH, Runquist JA, Holub A, Miziorko HM
Title The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9477947
Journal Biochemistry
Year 1998
Volume 37
Pages 1221-6
Authors Runquist JA, Harrison DH, Miziorko HM
Title Functional evaluation of invariant arginines situated in the mobile lid domain of phosphoribulokinase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 10563798
Journal Biochemistry
Year 1999
Volume 38
Pages 15157-65
Authors Kung G, Runquist JA, Miziorko HM, Harrison DH
Title Identification of the allosteric regulatory site in bacterial phosphoribulokinase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 10800594
Journal Adv Enzymol Relat Areas Mol Biol
Year 2000
Volume 74
Pages 95-127
Authors Miziorko HM
Title Phosphoribulokinase: current perspectives on the structure/function basis for regulation and catalysis.
Related PDB
Related UniProtKB

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.

Created Updated
2002-05-31 2009-02-26