Orotidine 5'-phosphate decarboxylase - Methanobacterium thermoautotrophicum (strain Delta H)

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O26232 (PYRF_METTH) Reviewed, UniProtKB/Swiss-Prot

Last modified November 16, 2011. Version 92. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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 (strain Delta H)

Taxonomic identifier

187420 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanobacteria › Methanobacteriales › Methanobacteriaceae › Methanothermobacter

Protein attributes

Sequence length	228 AA.
Sequence status	Complete.
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_A
Catalytic activity	Orotidine 5'-phosphate = UMP + CO₂. HAMAP MF_01200_A
Pathway	Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. HAMAP MF_01200_A
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 Reference proteome
Gene Ontology (GO)
Biological process	'de novo' UMP biosynthetic process Inferred from electronic annotation. Source: InterPro 'de novo' pyrimidine base biosynthetic process Inferred from electronic annotation. Source: InterPro
Molecular function	orotidine-5'-phosphate decarboxylase activity Inferred from electronic annotation. Source: EC
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_A

PRO_0000134612

Regions

Region

70 – 79

Substrate binding HAMAP MF_01200_A

Region

180 – 190

Substrate binding HAMAP MF_01200_A

Sites

Active site

Proton donor

Binding site

Substrate

Binding site

Substrate

Binding site

127

Substrate

Binding site

202

Substrate; via amide nitrogen

Binding site

203

Substrate

Secondary structure

228

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

O26232 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: A7B65D94C8663D78
Show »

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

« Hide

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. 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000666 Genomic DNA. Translation: AAB84635.1.

PIR

F69038.

RefSeq

NP_275272.1. NC_000916.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]
3G18	X-ray	1.60	A/B	1-228	[»]
3G1A	X-ray	1.50	A/B	1-228	[»]
3G1D	X-ray	1.50	A/B	1-228	[»]
3G1F	X-ray	2.50	A/B/C/D/E/F/G/H/I/J/K/L/M	1-228	[»]
3G1H	X-ray	2.30	A/B/C/D/E/F/G/H/I/J/K/L/M	1-228	[»]
3G1S	X-ray	1.40	A/B	1-228	[»]
3G1V	X-ray	1.30	A/B	1-228	[»]
3G1X	X-ray	1.55	A/B	1-228	[»]
3G1Y	X-ray	1.40	A/B	1-228	[»]
3G22	X-ray	1.50	A/B	1-228	[»]
3G24	X-ray	1.50	A/B	1-228	[»]
3LHT	X-ray	1.35	A/B	1-228	[»]
3LHU	X-ray	1.60	A/B	1-228	[»]
3LHV	X-ray	1.35	A/B/C/D	1-228	[»]
3LHW	X-ray	1.35	A/B	1-228	[»]
3LHY	X-ray	1.40	A/B	1-228	[»]
3LHZ	X-ray	1.40	A/B	1-228	[»]
3LI0	X-ray	1.50	A/B	1-228	[»]
3LI1	X-ray	1.35	A/B	1-228	[»]
3LLD	X-ray	1.45	A/B	1-228	[»]
3LLF	X-ray	1.30	A/B	1-228	[»]
3LTP	X-ray	1.40	A/B	1-228	[»]
3LTS	X-ray	1.43	A/B	1-228	[»]
3LTY	X-ray	1.50	A/B	1-228	[»]
3LV5	X-ray	1.44	A/B	1-228	[»]
3LV6	X-ray	1.45	A/B	1-228	[»]
3M1Z	X-ray	1.42	A/B	1-228	[»]
3M41	X-ray	1.40	A/B	1-228	[»]
3M43	X-ray	1.30	A/B	1-228	[»]
3M44	X-ray	1.40	A/B	1-228	[»]
3M47	X-ray	1.20	A/B	1-228	[»]
3M5X	X-ray	1.40	A/B	1-228	[»]
3M5Y	X-ray	1.46	A/B	1-228	[»]
3M5Z	X-ray	1.35	A/B	1-228	[»]
3NQ6	X-ray	1.49	A/B	1-228	[»]
3NQ7	X-ray	1.44	A/B	1-228	[»]
3NQA	X-ray	1.40	A/B	1-228	[»]
3NQC	X-ray	1.53	A/B	1-228	[»]
3NQD	X-ray	1.42	A/B	1-228	[»]
3NQE	X-ray	1.42	A/B	1-228	[»]
3NQF	X-ray	1.31	A/B	1-228	[»]
3NQG	X-ray	1.42	A/B	1-228	[»]
3NQM	X-ray	1.32	A/B	1-228	[»]
3P5Y	X-ray	1.60	A/B	1-228	[»]
3P5Z	X-ray	1.30	A/B	1-228	[»]
3P60	X-ray	1.40	A/B	1-228	[»]
3P61	X-ray	1.40	A/B	1-228	[»]
3PBU	X-ray	1.30	A/B	1-228	[»]
3PBV	X-ray	1.30	A/B	1-228	[»]
3PBW	X-ray	1.30	A/B	1-228	[»]
3PBY	X-ray	1.30	A/B	1-228	[»]
3PC0	X-ray	1.30	A/B	1-228	[»]
3SIZ	X-ray	1.32	A/B	1-228	[»]
3SJ3	X-ray	1.26	A/B	1-228	[»]
3SY5	X-ray	1.32	A/B	1-228	[»]

ProteinModelPortal

O26232.

SMR

O26232. Positions 9-228.

ModBase

Search...

Protein-protein interaction databases

STRING

O26232.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1470090.

GenomeReviews

Gene locus MTH_129 in contig AE000666_GR.

KEGG

mth:MTH129.

NMPDR

fig|187420.1.peg.127.

Phylogenomic databases

eggNOG

arNOG05213.

HOGENOM

HBG625253.

OMA

TEMSHPG.

PhylomeDB

O26232.

ProtClustDB

CLSK797833.

Enzyme and pathway databases

BioCyc

MTHE187420:MTH129-MONOMER.

Family and domain databases

HAMAP

MF_01200_A. OMPdecase_type1_A.
[Tree]

InterPro

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

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.

K01591.

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...

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:	November 16, 2011
This is version 92 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents