DB code: S00288

RLCP classification 2.40.48000.390 : Phosphorolysis
CATH domain 3.40.50.2020 : Rossmann fold Catalytic domain
E.C. 2.4.2.10
CSA 1oro
M-CSA 1oro
MACiE

CATH domain Related DB codes (homologues)
3.40.50.2020 : Rossmann fold S00289 S00287 D00131

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P08870 Orotate phosphoribosyltransferase
OPRT
OPRTase
EC 2.4.2.10
NP_462633.1 (Protein)
NC_003197.1 (DNA/RNA sequence)
PF00156 (Pribosyltran)
[Graphical View]
P0A7E3 Orotate phosphoribosyltransferase
OPRT
OPRTase
EC 2.4.2.10
NP_418099.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491791.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00156 (Pribosyltran)
[Graphical View]

KEGG enzyme name
orotate phosphoribosyltransferase
orotidylic acid phosphorylase
orotidine-5'-phosphate pyrophosphorylase
OPRTase
orotate phosphoribosyl pyrophosphate transferase
orotic acid phosphoribosyltransferase
orotidine 5'-monophosphate pyrophosphorylase
orotidine monophosphate pyrophosphorylase
orotidine phosphoribosyltransferase
orotidylate phosphoribosyltransferase
orotidylate pyrophosphorylase
orotidylic acid pyrophosphorylase
orotidylic phosphorylase
orotidylic pyrophosphorylase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P08870 PYRE_SALTY Orotidine 5''-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate. Homodimer. Magnesium. Manganese can replace magnesium as the divalent metal. The role of metal is to bind PRPP and form a MgPRPP complex which then serves as substrate for OPRTase.
P0A7E3 PYRE_ECOLI Orotidine 5''-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate. Homodimer. Magnesium (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00240 Pyrimidine metabolism
MAP00983 Drug metabolism - other enzymes

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C01103 C00013 C00295 C00119 C00105 C00011
E.C.
Compound Magnesium Orotidine 5'-phosphate Pyrophosphate Orotate 5-Phospho-alpha-D-ribose 1-diphosphate UMP CO2
Type divalent metal (Ca2+, Mg2+) amide group,carbohydrate,nucleotide phosphate group/phosphate ion amide group,aromatic ring (with nitrogen atoms),carboxyl group carbohydrate,phosphate group/phosphate ion amide group,nucleotide others
ChEBI 18420
15842
29888
16742
17111
16695
16526
PubChem 888
160617
1023
21961011
967
7339
6030
280
1oprA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Bound:ORO Bound:PRP Unbound Unbound
1oroA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:SO4 Unbound Unbound Unbound Unbound
1oroB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:SO4 Unbound Unbound Unbound Unbound
1stoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:OMP Unbound Unbound Unbound Unbound Unbound
1lh0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ORO Unbound Unbound Unbound
1lh0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Bound:ORO Bound:PRP Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1oprA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 103 LYS 73;ASP 124;ASP 125(Mg2+ binding)
1oroA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 103 LYS 73;ASP 124;ASP 125(Mg2+ binding)
1oroB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 73;ASP 124;ASP 125(Mg2+ binding) invisible 102-108
1stoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 73;ASP 124;ASP 125(Mg2+ binding) invisible 103-107
1lh0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 1103 LYS 1073;ASP 1124;ASP 1125(Mg2+ binding)
1lh0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 2073;ASP 2124;ASP 2125(Mg2+ binding) invisible 2102-2108

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[7]
Fig.3, p.19-20 2

References
[1]
Resource
Comments
Medline ID
PubMed ID 2271660
Journal Biochemistry
Year 1990
Volume 29
Pages 10480-7
Authors Bhatia MB, Vinitsky A, Grubmeyer C
Title Kinetic mechanism of orotate phosphoribosyltransferase from Salmonella typhimurium.
Related PDB
Related UniProtKB P08870
[2]
Resource
Comments
Medline ID
PubMed ID 8376388
Journal J Biol Chem
Year 1993
Volume 268
Pages 20299-304
Authors Grubmeyer C, Segura E, Dorfman R
Title Active site lysines in orotate phosphoribosyltransferase.
Related PDB
Related UniProtKB P08870
[3]
Resource
Comments
Medline ID
PubMed ID 8312245
Journal Biochemistry
Year 1994
Volume 33
Pages 1287-94
Authors Scapin G, Grubmeyer C, Sacchettini JC
Title Crystal structure of orotate phosphoribosyltransferase.
Related PDB 1sto
Related UniProtKB P08870
[4]
Resource
Comments
Medline ID
PubMed ID 7545004
Journal Biochemistry
Year 1995
Volume 34
Pages 10744-54
Authors Scapin G, Ozturk DH, Grubmeyer C, Sacchettini JC
Title The crystal structure of the orotate phosphoribosyltransferase complexed with orotate and alpha-D-5-phosphoribosyl-1-pyrophosphate.
Related PDB 1opr
Related UniProtKB P08870
[5]
Resource
Comments
Medline ID
PubMed ID 7545005
Journal Biochemistry
Year 1995
Volume 34
Pages 10755-63
Authors Ozturk DH, Dorfman RH, Scapin G, Sacchettini JC, Grubmeyer C
Title Locations and functional roles of conserved lysine residues in Salmonella typhimurium orotate phosphoribosyltransferase.
Related PDB
Related UniProtKB P08870
[6]
Resource
Comments
Medline ID
PubMed ID 7545006
Journal Biochemistry
Year 1995
Volume 34
Pages 10764-70
Authors Ozturk DH, Dorfman RH, Scapin G, Sacchettini JC, Grubmeyer C
Title Structure and function of Salmonella typhimurium orotate phosphoribosyltransferase: protein complementation reveals shared active sites.
Related PDB
Related UniProtKB P08870
[7]
Resource
Comments
Medline ID
PubMed ID 8555167
Journal Biochemistry
Year 1996
Volume 35
Pages 14-21
Authors Tao W, Grubmeyer C, Blanchard JS
Title Transition state structure of Salmonella typhimurium orotate phosphoribosyltransferase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 8620002
Journal Biochemistry
Year 1996
Volume 35
Pages 3803-9
Authors Henriksen A, Aghajari N, Jensen KF, Gajhede M
Title A flexible loop at the dimer interface is a part of the active site of the adjacent monomer of Escherichia coli orotate phosphoribosyltransferase.
Related PDB 1oro
Related UniProtKB P0A7E3

Comments
The literature [4] indicated that the ribose of substrate will move in spite of the slight movement of the overall strucuture of the OPRTase itself (see Figs. 6 and 7). The literature [5] indicated that Lys103 plays an essential role in catalysis, although this residue is away from the active site. One possible role for Lys103 is to serve as an acid to protonate the leaving pyrophosphate group or as a base to deprotonate the incoming orotate. Another possible role is to shield the active site from solvent, as the oxocarbonium transition state is unstable with solvent [5]. Moreover, this literature indicated that Lys73 extends into the active site, and a conformational change allows it to interact with either the 5'-phosphate of OMP or the 2-hydroxyl and alpha-phosphoryl oxgen of PRPP in the respective complexes. The literature [6] indicated that the active site of OPRTase requires Asp125 from one subunit and Lys103 from the adjacent subunit of heterodimer.
According to [7], the partial C1'-O4' bond cleavage and double bond formation in C1'-O4' argue that the reaction undergoes an SN1-like mechanism, with a posiively-charged oxocarbonium ion in the transition state. As the oxocarbonium ion is reactive and unstable, it needs to be stablized by some negative charge in the enzyme active site. The paired Asp125 and Asp124 are highly conserved, but they are away from the oxocarbonium ion, which is difficult to stabilize.
The interaction of Lys73 with 5'-phosphate is disrupted by pyrophosphate binding, and this could initiates catalysis, thus preventing nonproductive hydrolysis via solvent capture of the oxocarbonium ion [7]. This loss of the 5'-phosphate-Lys73 interaction also may allow for the interaction between the 5'-phosphate and phosphate binding loop interactions to become stronger and initiate the movement of the ribose 5'-phosphate ring away from the orotate ring. The O4' ring oxygen initiates oxocarbonium ion formation by electron donation into the C1'-O4' bond, with subsequent lengthening of the C1'-N1 bond. Both orotate keto oxygen bond lengths have lengthened, dispersing the buildup of negative charge on the orotate ring [7]. The bipolar tansition state, with the negative charge of orotate ring and the positive charge of the ribose ring, is energetically stabilized via both "intra-molecular" and enzyme-transition state interactions [7].
As the intra-molecular stabilization decreases, and as the 5'-phosphate is pulled further into the phosphate binding loop, the swinging movement of the ribosyl 5'-phosphate caation is likely intiated by the long-range electrostatic attraction between the oxocarbonium ion and Asp125 [7]. The approach og the face of the oxocarbonium ion to bound pyrophoshate results in the formation of the covalent C1-O-PPi bond in the alpha-anomeric configuration [7].
The litarture [8] indicated that the flexible loop region (residues 102-108) is important for catalysis. The movement of this loop in association with the movement of OMP is vital to catalysis.

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