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O26232 (PYRF_METTH) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 111. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismMethanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum) [Reference proteome] [HAMAP]
Taxonomic identifier187420 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaMethanobacteriaMethanobacterialesMethanobacteriaceaeMethanothermobacter

Protein attributes

Sequence length228 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). HAMAP-Rule MF_01200_A

Catalytic activity

Orotidine 5'-phosphate = UMP + CO2. HAMAP-Rule MF_01200_A

Pathway

Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. HAMAP-Rule 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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 228228Orotidine 5'-phosphate decarboxylase HAMAP-Rule MF_01200_A
PRO_0000134612

Regions

Region70 – 7910Substrate binding HAMAP-Rule MF_01200_A
Region180 – 19011Substrate binding HAMAP-Rule MF_01200_A

Sites

Active site721Proton donor
Binding site201Substrate
Binding site421Substrate
Binding site1271Substrate
Binding site2021Substrate; via amide nitrogen
Binding site2031Substrate

Secondary structure

............................................. 228
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O26232 [UniParc].

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

FASTA22824,915
        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' 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. expand/collapse author list , 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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / 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] [Europe PMC] [Abstract]
Cited for: CRYSTALLIZATION.
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / 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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEX WITH 6-AZAUMP, SUBUNIT.
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / 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] [Europe PMC] [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: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / 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] [Europe PMC] [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: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / 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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF COMPLEX WITH BMP, SUBUNIT.
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE000666 Genomic DNA. Translation: AAB84635.1.
PIRF69038.
RefSeqNP_275272.1. NC_000916.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1DV7X-ray1.80A2-228[»]
1DVJX-ray1.50A/B/C/D2-226[»]
1KLYX-ray1.50A1-228[»]
1KLZX-ray1.50A1-228[»]
1KM0X-ray1.70A/B/C/D1-226[»]
1KM1X-ray1.60A/B1-226[»]
1KM2X-ray1.50A1-226[»]
1KM3X-ray1.50A1-226[»]
1KM4X-ray1.50A1-226[»]
1KM5X-ray1.50A1-226[»]
1KM6X-ray1.50A1-226[»]
1LOLX-ray1.90A/B2-226[»]
1LOQX-ray1.50A2-228[»]
1LORX-ray1.60A2-228[»]
1LOSX-ray1.90A/B/C/D2-228[»]
1LP6X-ray1.90A/B2-226[»]
1X1ZX-ray1.45A/B1-225[»]
2E6YX-ray1.60A/B1-225[»]
2ZZ1X-ray1.57A/B1-225[»]
2ZZ2X-ray1.53A/B1-225[»]
2ZZ3X-ray1.80A/B1-225[»]
2ZZ4X-ray1.67A/B1-225[»]
2ZZ5X-ray1.56A/B1-225[»]
2ZZ6X-ray1.66A/B1-225[»]
2ZZ7X-ray1.58A1-225[»]
3G18X-ray1.60A/B1-228[»]
3G1AX-ray1.50A/B1-228[»]
3G1DX-ray1.50A/B1-228[»]
3G1FX-ray2.50A/B/C/D/E/F/G/H/I/J/K/L/M1-228[»]
3G1HX-ray2.30A/B/C/D/E/F/G/H/I/J/K/L/M1-228[»]
3G1SX-ray1.40A/B1-228[»]
3G1VX-ray1.30A/B1-228[»]
3G1XX-ray1.55A/B1-228[»]
3G1YX-ray1.40A/B1-228[»]
3G22X-ray1.50A/B1-228[»]
3G24X-ray1.50A/B1-228[»]
3LHTX-ray1.35A/B1-228[»]
3LHUX-ray1.60A/B1-228[»]
3LHVX-ray1.35A/B/C/D1-228[»]
3LHWX-ray1.35A/B1-228[»]
3LHYX-ray1.40A/B1-228[»]
3LHZX-ray1.40A/B1-228[»]
3LI0X-ray1.50A/B1-228[»]
3LI1X-ray1.35A/B1-228[»]
3LLDX-ray1.45A/B1-228[»]
3LLFX-ray1.30A/B1-228[»]
3LTPX-ray1.40A/B1-228[»]
3LTSX-ray1.43A/B1-228[»]
3LTYX-ray1.50A/B1-228[»]
3LV5X-ray1.44A/B1-228[»]
3LV6X-ray1.45A/B1-228[»]
3M1ZX-ray1.42A/B1-228[»]
3M41X-ray1.40A/B1-228[»]
3M43X-ray1.30A/B1-228[»]
3M44X-ray1.40A/B1-228[»]
3M47X-ray1.20A/B1-228[»]
3M5XX-ray1.40A/B1-228[»]
3M5YX-ray1.46A/B1-228[»]
3M5ZX-ray1.35A/B1-228[»]
3NQ6X-ray1.49A/B1-228[»]
3NQ7X-ray1.44A/B1-228[»]
3NQAX-ray1.40A/B1-228[»]
3NQCX-ray1.53A/B1-228[»]
3NQDX-ray1.42A/B1-228[»]
3NQEX-ray1.42A/B1-228[»]
3NQFX-ray1.31A/B1-228[»]
3NQGX-ray1.42A/B1-228[»]
3NQMX-ray1.32A/B1-228[»]
3P5YX-ray1.60A/B1-228[»]
3P5ZX-ray1.30A/B1-228[»]
3P60X-ray1.40A/B1-228[»]
3P61X-ray1.40A/B1-228[»]
3PBUX-ray1.30A/B1-228[»]
3PBVX-ray1.30A/B1-228[»]
3PBWX-ray1.30A/B1-228[»]
3PBYX-ray1.30A/B1-228[»]
3PC0X-ray1.30A/B1-228[»]
3QEZX-ray1.54A/B1-228[»]
3QF0X-ray1.34A/B1-228[»]
3QMRX-ray1.32A/B1-228[»]
3QMSX-ray1.32A/B1-228[»]
3QMTX-ray1.32A/B1-228[»]
3RLUX-ray1.49A/B1-228[»]
3RLVX-ray1.42A/B1-228[»]
3SECX-ray1.70A1-226[»]
3SGUX-ray1.70A1-226[»]
3SIZX-ray1.32A/B1-228[»]
3SJ3X-ray1.26A/B1-228[»]
3SSJX-ray1.40A1-226[»]
3SW6X-ray1.50A1-226[»]
3SY5X-ray1.32A/B1-228[»]
3THQX-ray1.50A/B1-226[»]
3V1PX-ray1.37A/B1-228[»]
3W07X-ray1.03A1-225[»]
3WJWX-ray1.59A1-228[»]
3WJXX-ray1.23A1-228[»]
3WJYX-ray1.72A1-228[»]
3WJZX-ray1.39A1-228[»]
3WK0X-ray1.41A1-228[»]
3WK1X-ray1.60A1-228[»]
3WK2X-ray1.69A1-228[»]
3WK3X-ray1.26A1-228[»]
4FX6X-ray1.53M/N1-228[»]
4FX8X-ray1.94A/B1-228[»]
4FXRX-ray1.71A/B1-228[»]
4GC4X-ray1.42A/B1-228[»]
4LC6X-ray1.32A/B1-228[»]
4LC8X-ray1.32A/B1-228[»]
4NT0X-ray1.77A/B1-228[»]
4NUWX-ray1.59A/B1-228[»]
4NX5X-ray1.59A/B1-228[»]
4O11X-ray1.59A/B1-228[»]
4O8RX-ray2.29A/B/C/D/E/F/G/H/I/J/K/L/M1-228[»]
ProteinModelPortalO26232.
SMRO26232. Positions 9-228.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING187420.MTH129.

Chemistry

BindingDBO26232.
ChEMBLCHEMBL5688.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAB84635; AAB84635; MTH_129.
GeneID1470090.
KEGGmth:MTH129.

Phylogenomic databases

eggNOGCOG0284.
KOK01591.
OMATEMSHPG.
ProtClustDBCLSK797833.

Enzyme and pathway databases

BioCycMTHE187420:GJNM-129-MONOMER.
UniPathwayUPA00070; UER00120.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
HAMAPMF_01200_A. OMPdecase_type1_A.
InterProIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMSSF51366. SSF51366. 1 hit.
TIGRFAMsTIGR01740. pyrF. 1 hit.
PROSITEPS00156. OMPDECASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO26232.
PROO26232.

Entry information

Entry namePYRF_METTH
AccessionPrimary (citable) accession number: O26232
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: March 19, 2014
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways