P03962 (PYRF_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Orotidine 5'-phosphate decarboxylase
EC=4.1.1.23

Alternative name(s):
OMP decarboxylase
Short name=OMPDCase
Short name=OMPdecase
Uridine 5'-monophosphate synthase
Short name=UMP synthase

Gene names

Name:	URA3
Ordered Locus Names:	YEL021W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	267 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	Orotidine 5'-phosphate = UMP + CO2.
Pathway	Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2.
Sequence similarities	Belongs to the OMP decarboxylase family.
Sequence caution	The sequence CAA25010.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Molecular function	Decarboxylase Lyase
PTM	Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	'de novo' UMP biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway 'de novo' pyrimidine nucleobase biosynthetic process Inferred from mutant phenotype PubMed 4550660PubMed 5651325. Source: SGD UMP biosynthetic process Inferred from direct assay PubMed 2061334. Source: SGD
Cellular_component	cytosol Inferred from direct assay PubMed 18812321. Source: SGD
Molecular_function	orotidine-5'-phosphate decarboxylase activity Inferred from direct assay PubMed 2061334. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 267

267

Orotidine 5'-phosphate decarboxylase

PRO_0000134692

Regions

Region

59 – 61

3

Substrate binding

Region

91 – 100

10

Substrate binding

Sites

Active site

93

1

Proton donor

Binding site

37

1

Substrate

Binding site

217

1

Substrate

Binding site

235

1

Substrate

Amino acid modifications

Modified residue

219

1

Phosphothreonine Ref.9

Modified residue

228

1

Phosphoserine Ref.9

Cross-link

93

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.8

Cross-link

209

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.8

Cross-link

253

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.8

Natural variations

Natural variant

160

1

A → S in strain: +D4.

Experimental info

Mutagenesis

59

1

K → A: Reduces Kcat 100-fold. Reduces substrate affinity 900-fold. Ref.7

Mutagenesis

91

1

D → A: Reduces activity over 100000-fold. Ref.7

Mutagenesis

93

1

K → A: Reduces activity over 100000-fold. Ref.7

Mutagenesis

96

1

D → A: Reduces Kcat over 100000-fold. Reduces substrate affinity 11-fold. Ref.7

Mutagenesis

215

1

Q → A: No effect. Ref.7

Sequence conflict

71 – 73

3

EGT → RIR in AAA35199. Ref.4

Secondary structure

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267

Helix Strand Turn

Details...

Helix

6 – 12

7

Helix

16 – 28

13

Beta strand

32 – 35

4

Helix

41 – 51

11

Helix

52 – 54

3

Beta strand

56 – 60

5

Helix

62 – 64

3

Turn

70 – 73

4

Helix

74 – 84

11

Beta strand

87 – 94

8

Helix

98 – 106

9

Turn

108 – 110

3

Helix

112 – 115

4

Beta strand

117 – 122

6

Helix

123 – 125

3

Helix

128 – 140

13

Beta strand

146 – 150

5

Helix

162 – 172

11

Turn

176 – 178

3

Beta strand

179 – 183

5

Helix

191 – 193

3

Beta strand

198 – 201

4

Beta strand

203 – 205

3

Turn

208 – 210

3

Helix

214 – 216

3

Beta strand

217 – 219

3

Helix

220 – 225

6

Beta strand

229 – 233

5

Helix

235 – 237

3

Helix

244 – 262

19

Sequences

	Sequence		Length	Mass (Da)
	P03962 [UniParc]. Last modified February 1, 1995. Version 2. Checksum: D63EF9877BD0F984	FASTA	267	29,240
	10 20 30 40 50 60 MSKATYKERA ATHPSPVAAK LFNIMHEKQT NLCASLDVRT TKELLELVEA LGPKICLLKT 70 80 90 100 110 120 HVDILTDFSM EGTVKPLKAL SAKYNFLLFE DRKFADIGNT VKLQYSAGVY RIAEWADITN 130 140 150 160 170 180 AHGVVGPGIV SGLKQAAEEV TKEPRGLLML AELSCKGSLA TGEYTKGTVD IAKSDKDFVI 190 200 210 220 230 240 GFIAQRDMGG RDEGYDWLIM TPGVGLDDKG DALGQQYRTV DDVVSTGSDI IIVGRGLFAK 250 260 GRDAKVEGER YRKAGWEAYL RRCGQQN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure and function of the yeast URA3 gene: expression in Escherichia coli." Rose M., Grisafi P., Botstein D. Gene 29:113-124(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: +D4 and ATCC 28383 / FL100 / VTT C-80102.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W. Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	Holtz A., Lou Y. Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[5]	"Transcription terminator-like element within a Saccharomyces cerevisiae promoter region." Yarger J.G., Armilei G., Gorman M.C. Mol. Cell. Biol. 6:1095-1101(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-73.
[6]	"Structure and function of the yeast URA3 gene. Differentially regulated expression of hybrid beta-galactosidase from overlapping coding sequences in yeast." Rose M., Botstein D. J. Mol. Biol. 170:883-904(1983) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-11.
[7]	"Dissecting a charged network at the active site of orotidine-5'-phosphate decarboxylase." Miller B.G., Snider M.J., Wolfenden R., Short S.A. J. Biol. Chem. 276:15174-15176(2001) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF LYS-59; ASP-91; LYS-93; ASP-96 AND GLN-215.
[8]	"A proteomics approach to understanding protein ubiquitination." Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P. Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-93; LYS-209 AND LYS-253, MASS SPECTROMETRY. Strain: SUB592.
[9]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-219 AND SER-228, MASS SPECTROMETRY.
[10]	"Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog." Miller B.G., Hassell A.M., Wolfenden R., Milburn M.V., Short S.A. Proc. Natl. Acad. Sci. U.S.A. 97:2011-2016(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH TRANSITION STATE ANALOG.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

K02206 Genomic DNA. Translation: AAA34824.1.
K02207 Genomic DNA. Translation: AAA34825.1.
U18530 Genomic DNA. Translation: AAB64498.1.
U89671 Genomic DNA. Translation: AAB49978.1.
M12926 Genomic DNA. Translation: AAA35199.1.
X00191 Genomic DNA. Translation: CAA25010.1. Different initiation.
U89927 Genomic DNA. Translation: AAB64383.1.
U63018 Genomic DNA. Translation: AAC53678.1.
BK006939 Genomic DNA. Translation: DAA07631.1.

PIR

DEBYOP. A01082.
DCBYOF. S05735.

RefSeq

NP_010893.3. NM_001178836.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DQW	X-ray	2.10	A/B/C/D	3-266	[»]
1DQX	X-ray	2.40	A/B/C/D	3-266	[»]
3GDK	X-ray	2.00	A/B/C/D	1-267	[»]
3GDL	X-ray	1.65	A/B	1-267	[»]
3GDM	X-ray	1.60	A/B	1-267	[»]
3GDR	X-ray	1.90	A/B/C/D	1-267	[»]
3GDT	X-ray	1.60	A/B/C/D	1-267	[»]

ProteinModelPortal

P03962.

SMR

P03962. Positions 3-263.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6576N.

IntAct

P03962. 1 interaction.

MINT

MINT-410591.

STRING

4932.YEL021W.

Proteomic databases

PaxDb

P03962.

PeptideAtlas

P03962.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YEL021W; YEL021W; YEL021W.

GeneID

856692.

KEGG

sce:YEL019C.
sce:YEL021W.

Organism-specific databases

CYGD

YEL021w.

SGD

S000000747. URA3.

Phylogenomic databases

eggNOG

COG0284.

GeneTree

ENSGT00390000001856.

HOGENOM

HOG000213905.

KO

K01591.

OMA

DITNAHG.

OrthoDB

EOG4K9FN7.

Enzyme and pathway databases

SABIO-RK

P03962.

UniPathway

UPA00070; UER00120.

Gene expression databases

Genevestigator

P03962.

GermOnline

YEL021W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

InterPro

IPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]

Pfam

PF00215. OMPdecase. 1 hit.
[Graphical view]

SMART

SM00934. OMPdecase. 1 hit.
[Graphical view]

SUPFAM

SSF51366. RibP_bind_barrel. 1 hit.

TIGRFAMs

TIGR01740. pyrF. 1 hit.

PROSITE

PS00156. OMPDECASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P03962.

ChEMBL

CHEMBL4858.

EvolutionaryTrace

P03962.

NextBio

982739.

Entry information

Entry name

PYRF_YEAST

Accession

Primary (citable) accession number: P03962
Secondary accession number(s): D3DLM7

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 23, 1986
Last sequence update:	February 1, 1995
Last modified:	April 3, 2013
This is version 141 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program