Reviewed, UniProtKB/Swiss-Prot O26232 (PYRF_METTH)

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

Gene names

Name:	pyrF
Ordered Locus Names:	MTH_129

Organism

Methanobacterium thermoautotrophicum [Complete proteome] [HAMAP]

Taxonomic identifier

187420 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanobacteria › Methanobacteriales › Methanobacteriaceae › Methanothermobacter

Protein attributes

Sequence length	228 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). HAMAP MF_01200
Catalytic activity	Orotidine 5'-phosphate = UMP + CO2. HAMAP MF_01200
Pathway	Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from HCO(3)(-): step 6/6. HAMAP MF_01200
Subunit structure	Homodimer. Ref.3 Ref.4 Ref.5 Ref.6
Sequence similarities	Belongs to the OMP decarboxylase family. Type 1 subfamily.

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Molecular function	Decarboxylase Lyase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	'de novo' pyrimidine base biosynthetic process Inferred from electronic annotation. Source: InterPro pyrimidine nucleotide biosynthetic process Inferred from electronic annotation. Source: HAMAP
Molecular function	orotidine-5'-phosphate decarboxylase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 228

228

Orotidine 5'-phosphate decarboxylase HAMAP MF_01200

PRO_0000134612

Regions

Region

70 – 79

10

Substrate binding HAMAP MF_01200

Region

180 – 190

11

Substrate binding HAMAP MF_01200

Sites

Active site

72

1

Proton donor HAMAP MF_01200

Binding site

20

1

Substrate HAMAP MF_01200

Binding site

42

1

Substrate HAMAP MF_01200

Binding site

127

1

Substrate HAMAP MF_01200

Binding site

202

1

Substrate; via amide nitrogen HAMAP MF_01200

Binding site

203

1

Substrate HAMAP MF_01200

Secondary structure

1

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228

Helix Strand Turn

Details...

Helix

12 – 14

3

Beta strand

15 – 19

5

Helix

24 – 34

11

Helix

35 – 37

3

Beta strand

39 – 44

6

Helix

45 – 51

7

Helix

54 – 63

10

Beta strand

66 – 73

8

Helix

77 – 89

13

Beta strand

93 – 99

7

Helix

103 – 116

14

Beta strand

119 – 123

5

Helix

129 – 132

4

Helix

135 – 149

15

Beta strand

153 – 155

3

Helix

161 – 171

11

Beta strand

173 – 179

7

Helix

189 – 192

4

Turn

193 – 195

3

Beta strand

197 – 201

5

Helix

203 – 206

4

Beta strand

208 – 210

3

Helix

211 – 223

13

Sequences

	Sequence		Length	Mass (Da)
	O26232-1 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: A7B65D94C8663D78	FASTA	228	24,915
	10 20 30 40 50 60 MRSRRVDVMD VMNRLILAMD LMNRDDALRV TGEVREYIDT VKIGYPLVLS EGMDIIAEFR 70 80 90 100 110 120 KRFGCRIIAD FKVADIPETN EKICRATFKA GADAIIVHGF RGADSVRACL NVAEEMGREV 130 140 150 160 170 180 FLLTEMSHPG AEMFIQGAAD EIARMGVDLG VKNYVGPSTR PERLSRLREI IGQDSFLISP 190 200 210 220 GVGAQGGDPG ETLRFADAII VGRSIYLADN PAAAAAGIIE SIKDLLNP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics." Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H.-M., Dubois J., Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K., Harrison D., Hoang L., Keagle P., Lumm W., Pothier B., Qiu D., Spadafora R., Vicare R. , Wang Y., Wierzbowski J., Gibson R., Jiwani N., Caruso A., Bush D., Safer H., Patwell D., Prabhakar S., McDougall S., Shimer G., Goyal A., Pietrovski S., Church G.M., Daniels C.J., Mao J.-I., Rice P., Noelling J., Reeve J.N. J. Bacteriol. 179:7135-7155(1997) [PubMed: 9371463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Delta H.
[2]	"Purification, crystallization and preliminary X-ray study of orotidine 5'-monophosphate decarboxylase." Wu N., Christendat D., Dharamsi A., Pai E.F. Acta Crystallogr. D 56:912-914(2000) [PubMed: 10930842] [Abstract] Cited for: CRYSTALLIZATION. Strain: Delta H.
[3]	"Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase." Wu N., Mo Y., Gao J., Pai E.F. Proc. Natl. Acad. Sci. U.S.A. 97:2017-2022(2000) [PubMed: 10681441] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEX WITH 6-AZAUMP, SUBUNIT. Strain: Delta H.
[4]	"Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography." Wu N., Gillon W., Pai E.F. Biochemistry 41:4002-4011(2002) [PubMed: 11900543] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF MUTANTS ALA-42; GLY-70; ALA-70; ALA-72; ALA-70/ALA-72; ASN-75; ALA-127 AND ALA-185 IN COMPLEX WITH DIFFERENT LIGANDS, SUBUNIT. Strain: Delta H.
[5]	"Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase." Wu N., Pai E.F. J. Biol. Chem. 277:28080-28087(2002) [PubMed: 12011084] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF COMPLEXES WITH BMP; CMP; UMP; XMP AND OF MUTANT DELTA ALA-203 IN COMPLEX WITH 6-AZAUMP, SUBUNIT. Strain: Delta H.
[6]	"An unprecedented twist to ODCase catalytic activity." Fujihashi M., Bello A.M., Poduch E., Wei L., Annedi S.C., Pai E.F., Kotra L.P. J. Am. Chem. Soc. 127:15048-15050(2005) [PubMed: 16248642] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF COMPLEX WITH BMP, SUBUNIT. Strain: Delta H.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AE000666 Genomic DNA. Translation: AAB84635.1.

PIR

F69038.

RefSeq

NP_275272.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DV7	X-ray	1.80	A	2-228	[»]
1DVJ	X-ray	1.50	A/B/C/D	2-226	[»]
1KLY	X-ray	1.50	A	1-228	[»]
1KLZ	X-ray	1.50	A	1-228	[»]
1KM0	X-ray	1.70	A/B/C/D	1-226	[»]
1KM1	X-ray	1.60	A/B	1-226	[»]
1KM2	X-ray	1.50	A	1-226	[»]
1KM3	X-ray	1.50	A	1-226	[»]
1KM4	X-ray	1.50	A	1-226	[»]
1KM5	X-ray	1.50	A	1-226	[»]
1KM6	X-ray	1.50	A	1-226	[»]
1LOL	X-ray	1.90	A/B	2-226	[»]
1LOQ	X-ray	1.50	A	2-228	[»]
1LOR	X-ray	1.60	A	2-228	[»]
1LOS	X-ray	1.90	A/B/C/D	2-228	[»]
1LP6	X-ray	1.90	A/B	2-226	[»]
1X1Z	X-ray	1.45	A/B	1-225	[»]
2E6Y	X-ray	1.60	A/B	1-225	[»]
2ZZ1	X-ray	1.57	A/B	1-225	[»]
2ZZ2	X-ray	1.53	A/B	1-225	[»]
2ZZ3	X-ray	1.80	A/B	1-225	[»]
2ZZ4	X-ray	1.67	A/B	1-225	[»]
2ZZ5	X-ray	1.56	A/B	1-225	[»]
2ZZ6	X-ray	1.66	A/B	1-225	[»]
2ZZ7	X-ray	1.58	A	1-225	[»]

ModBase

Search...

Genome annotation databases

GeneID

1470090.

GenomeReviews

Gene locus MTH_129 in contig AE000666_GR.

KEGG

mth:MTH129.

NMPDR

fig|187420.1.peg.127.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

O26232.

OMA

O26232. PSTRPER.

Enzyme and pathway databases

BioCyc

MTHE187420:MTH129-MON.

BRENDA

4.1.1.23. 270.

Family and domain databases

HAMAP

MF_01200.
[Tree]

InterPro

IPR013785. Aldolase_TIM.
IPR014732. OMPdecase_1_core.
IPR018089. OMPdecase_AS.
IPR001754. OMPdecase_core.
[Graphical view]

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.

Pfam

PF00215. OMPdecase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01740. pyrF. 1 hit.

PROSITE

PS00156. OMPDECASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

PYRF_METTH

Accession

Primary (citable) accession number: O26232

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	January 1, 1998
Last modified:	June 16, 2009
This is version 76 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)