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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

Orotidine 5'-phosphate = UMP + CO2.

Pathwayi: UMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes UMP from orotate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Orotate phosphoribosyltransferase (pyrE)
  2. Orotidine 5'-phosphate decarboxylase (pyrF)
This subpathway is part of the pathway UMP biosynthesis via de novo pathway, which is itself part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes UMP from orotate, the pathway UMP biosynthesis via de novo pathway and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei20Substrate1
Binding sitei42Substrate1
Active sitei72Proton donor1
Binding sitei127Substrate1
Binding sitei202Substrate; via amide nitrogen1
Binding sitei203Substrate1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BRENDAi4.1.1.23. 7219.
UniPathwayiUPA00070; UER00120.

Names & Taxonomyi

Protein namesi
Recommended name:
Orotidine 5'-phosphate decarboxylase (EC:4.1.1.23)
Alternative name(s):
OMP decarboxylase
Short name:
OMPDCase
Short name:
OMPdecase
Gene namesi
Name:pyrF
Ordered Locus Names:MTH_129
OrganismiMethanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum)
Taxonomic identifieri187420 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanobacteriaMethanobacterialesMethanobacteriaceaeMethanothermobacter
Proteomesi
  • UP000005223 Componenti: Chromosome

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL5688.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001346121 – 228Orotidine 5'-phosphate decarboxylaseAdd BLAST228

Interactioni

Subunit structurei

Homodimer.4 Publications

Protein-protein interaction databases

STRINGi187420.MTH129.

Chemistry databases

BindingDBiO26232.

Structurei

Secondary structure

1228
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 8Combined sources3
Helixi12 – 14Combined sources3
Beta strandi15 – 19Combined sources5
Helixi24 – 34Combined sources11
Helixi35 – 37Combined sources3
Beta strandi39 – 44Combined sources6
Helixi45 – 51Combined sources7
Helixi54 – 63Combined sources10
Beta strandi66 – 73Combined sources8
Helixi77 – 89Combined sources13
Beta strandi93 – 99Combined sources7
Helixi103 – 116Combined sources14
Beta strandi119 – 123Combined sources5
Helixi129 – 132Combined sources4
Helixi135 – 149Combined sources15
Beta strandi153 – 155Combined sources3
Beta strandi158 – 160Combined sources3
Helixi161 – 171Combined sources11
Beta strandi173 – 179Combined sources7
Helixi189 – 192Combined sources4
Turni193 – 195Combined sources3
Beta strandi197 – 201Combined sources5
Helixi203 – 206Combined sources4
Beta strandi208 – 210Combined sources3
Helixi211 – 224Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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/B1-226[»]
1LOQX-ray1.50A1-228[»]
1LORX-ray1.60A1-228[»]
1LOSX-ray1.90A/B/C/D1-228[»]
1LP6X-ray1.90A/B1-226[»]
1X1ZX-ray1.45A/B1-228[»]
2E6YX-ray1.60A/B1-228[»]
2ZZ1X-ray1.57A/B1-228[»]
2ZZ2X-ray1.53A/B1-228[»]
2ZZ3X-ray1.80A/B1-228[»]
2ZZ4X-ray1.67A/B1-228[»]
2ZZ5X-ray1.56A/B1-228[»]
2ZZ6X-ray1.66A/B1-228[»]
2ZZ7X-ray1.58A1-228[»]
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-ray1.03A1-228[»]
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[»]
4LW7X-ray1.42A/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[»]
ProteinModelPortaliO26232.
SMRiO26232.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO26232.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni70 – 79Substrate binding10
Regioni180 – 190Substrate bindingAdd BLAST11

Sequence similaritiesi

Phylogenomic databases

eggNOGiarCOG00081. Archaea.
COG0284. LUCA.
KOiK01591.
OMAiVTEMSHP.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_A. OMPdecase_type1_A. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTiSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMiSSF51366. SSF51366. 1 hit.
TIGRFAMsiTIGR01740. pyrF. 1 hit.
PROSITEiPS00156. OMPDECASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O26232-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRSRRVDVMD VMNRLILAMD LMNRDDALRV TGEVREYIDT VKIGYPLVLS
60 70 80 90 100
EGMDIIAEFR KRFGCRIIAD FKVADIPETN EKICRATFKA GADAIIVHGF
110 120 130 140 150
RGADSVRACL NVAEEMGREV FLLTEMSHPG AEMFIQGAAD EIARMGVDLG
160 170 180 190 200
VKNYVGPSTR PERLSRLREI IGQDSFLISP GVGAQGGDPG ETLRFADAII
210 220
VGRSIYLADN PAAAAAGIIE SIKDLLNP
Length:228
Mass (Da):24,915
Last modified:January 1, 1998 - v1
Checksum:iA7B65D94C8663D78
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000666 Genomic DNA. Translation: AAB84635.1.
PIRiF69038.

Genome annotation databases

EnsemblBacteriaiAAB84635; AAB84635; MTH_129.
KEGGimth:MTH_129.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000666 Genomic DNA. Translation: AAB84635.1.
PIRiF69038.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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/B1-226[»]
1LOQX-ray1.50A1-228[»]
1LORX-ray1.60A1-228[»]
1LOSX-ray1.90A/B/C/D1-228[»]
1LP6X-ray1.90A/B1-226[»]
1X1ZX-ray1.45A/B1-228[»]
2E6YX-ray1.60A/B1-228[»]
2ZZ1X-ray1.57A/B1-228[»]
2ZZ2X-ray1.53A/B1-228[»]
2ZZ3X-ray1.80A/B1-228[»]
2ZZ4X-ray1.67A/B1-228[»]
2ZZ5X-ray1.56A/B1-228[»]
2ZZ6X-ray1.66A/B1-228[»]
2ZZ7X-ray1.58A1-228[»]
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-ray1.03A1-228[»]
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[»]
4LW7X-ray1.42A/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[»]
ProteinModelPortaliO26232.
SMRiO26232.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi187420.MTH129.

Chemistry databases

BindingDBiO26232.
ChEMBLiCHEMBL5688.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB84635; AAB84635; MTH_129.
KEGGimth:MTH_129.

Phylogenomic databases

eggNOGiarCOG00081. Archaea.
COG0284. LUCA.
KOiK01591.
OMAiVTEMSHP.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BRENDAi4.1.1.23. 7219.

Miscellaneous databases

EvolutionaryTraceiO26232.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_A. OMPdecase_type1_A. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTiSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMiSSF51366. SSF51366. 1 hit.
TIGRFAMsiTIGR01740. pyrF. 1 hit.
PROSITEiPS00156. OMPDECASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPYRF_METTH
AccessioniPrimary (citable) accession number: O26232
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.