OMPdecaseOrotidine 5'-phosphate decarboxylase / HUMPS family |
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| SMART accession number: | SM00934 |
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| Description: | Orotidine 5'-phosphate decarboxylase (OMPdecase) (PUBMED:2835631), (PUBMED:1730672) catalyzes the last step in the de novo biosynthesis of pyrimidines, the decarboxylation of OMP into UMP. In higher eukaryotes OMPdecase is part, with orotate phosphoribosyltransferase, of a bifunctional enzyme, while the prokaryotic and fungal OMPdecases are monofunctional protein. |
| Interpro abstract (IPR001754): | Orotidine 5'-phosphate decarboxylase (OMPdecase) [(PUBMED:2835631), (PUBMED:1730672)] catalyses the last step in the de novo biosynthesis of pyrimidines, the decarboxylation of OMP into UMP. In higher eukaryotes OMPdecase is part, with orotate phosphoribosyltransferase, of a bifunctional enzyme, while the prokaryotic and fungal OMPdecases are monofunctional protein. Some parts of the sequence of OMPdecase are well conserved across species. The best conserved region is located in the N-terminal half of OMPdecases and is centred around a lysine residue which is essential for the catalytic function of the enzyme. This entry also includes enzymes such as 3-hexulose-6-phosphate synthase EC 4.1.2.43 and 3-keto-L-gulonate-6-phosphate decarboxylase EC 4.1.1.85. |
| GO process: | 'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207) |
| GO function: | orotidine-5'-phosphate decarboxylase activity (GO:0004590) |
| Family alignment: |
There are 2287 OMPdecase domains in 2287 proteins in SMART's nrdb database.
Click on the following links for more information.
- Evolution (species in which this domain is found)
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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes - Cellular role (predicted cellular role)
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Cellular role: metabolism
- Literature (relevant references for this domain)
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Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Kimsey HH, Kaiser D
- The orotidine-5'-monophosphate decarboxylase gene of Myxococcus xanthus.Comparison to the OMP decarboxylase gene family.
- J Biol Chem. 1992; 267: 819-24
- Display abstract
The nucleotide sequence of the Myxococcus xanthusorotidine-5'-monophosphate decarboxylase (OMP DCase) gene was determined.The derived protein sequence is not closely related to other prokaryoticOMP DCase sequences; nor is it closely related to any eukaryotic OMP DCasesequences. Progressive multiple alignment of the M. xanthus OMP DCaseprotein sequence with 19 other OMP DCase sequences revealed four conservedregions present in all 20 sequences. Ten entirely conserved residues werefound in these four regions and one region contains a tight cluster of 5conserved residues, certain of which may be catalytically active residues.A second open reading frame was found upstream of uraA and oriented in thesame direction as uraA. A stretch of 21 consecutive pyrimidine (C or T)residues were found in the intercistronic region between the potentialribosome-binding site of uraA and the UGA stop codon of the upstream openreading frame. RNA directly upstream of the pyrimidine run, including theUGA stop codon of the upstream open reading frame, could be folded into astable hairpin structure resembling Rho-independent terminators ofEscherichia coli. Expression of the uraA gene may be regulated by anintercistronic transcription termination mechanism.
- Jacquet M, Guilbaud R, Garreau H
- Sequence analysis of the DdPYR5-6 gene coding for UMP synthase inDictyostelium discoideum and comparison with orotate phosphoribosyltransferases and OMP decarboxylases.
- Mol Gen Genet. 1988; 211: 441-5
- Display abstract
A Dictyostelium discoideum DNA fragment that complements the ura3 and theura5 mutants of Saccharomyces cerevisiae has been sequenced. It containsan open reading frame of 478 codons capable of encoding a polypeptide ofmolecular weight 52475. This gene, named DdPYR5-6, encodes a bifunctionalprotein composed of the orotate phosphoribosyl transferase (OPRTase) andthe orotidine-5'-phosphate decarboxylase (OMPdecase) domains described forUMP synthase in mammals. The existence of separate domains for the twoactivities was suspected because deletion of the N-terminal coding segmentof the gene eliminated the ura5 but not the ura3 complementing activity.We have now confirmed that the two parts of the open reading frame sharehomology with known OPRTase and OMPdecase sequences. Several blocks ofsequence are conserved among OPRTase from bacteria, fungi and slime moldand one of them corresponds to the consensus sequence forphosphoribosylbinding sites. The OMPdecase domain shows extensivesimilarity with the yeast and Neurospora crassa enzymes, suggesting thatthey have evolved from an ancestral gene which was fused to the OPRTasegene in D. discoideum. It is less related to the bacterial enzyme but allthese sequences present conserved blocks of homology which could identifythe active site. The codon usage is strongly biased in a manner similar tothat found for other D. discoideum genes. The flanking DNA containshomopolymers of A and T and alternating sequences that are characteristicof the gene organization in D. discoideum.
- Structure (3D structures containing this domain)
3D Structures of OMPdecase domains in PDB
PDB code Main view Title 1dbt 
Crystal structure of orotidine 5'-monophosphate decarboxylase from bacillus subtilis complexed with ump 1dqw 
Crystal structure of orotidine 5'-phosphate decarboxylase 1dqx 
Crystal structure of orotidine 5'-phosphate decarboxylase complexed to 6-hydroxyuridine 5'-phosphate (bmp) 1dv7 
Crystal structure of orotidine monophosphate decarboxylase 1dvj 
Crystal structure of orotidine monophosphate decarboxylase complexed with 6-azaump 1eix 
Structure of orotidine 5'-monophosphate decarboxylase from e. coli, co-crystallised with the inhibitor bmp 1jjk 
Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase from e. coli causes a change in crystal contacts and space group 1kly 
Orotidine monophosphate decarboxylase d70g mutant complexed with 6-azaump 1klz 
Crystal structure of orotidine monophosphate decarboxylase mutant d70a complexed with ump 1km0 
Crystal structure of orotidine monophosphate decarboxylase mutant d70n complexed with 6-azaump 1km1 
Orotidine monophosphate decarboxylase mutant s127a crystal structure 1km2 
Crystal structure of orotidine monophosphate mutant q185a with 6-azaump 1km3 
Crystal structure of odcase mutant k42a complexed with 6- azaump 1km4 
Crystal structure of odcase mutant k72a complexed with ump 1km5 
Crystal structure of odcase mutant d75n complexed with 6- azaump 1km6 
Crystal structure of odcase mutant d70ak72a complexed with omp 1kv8 
Crystal structure of 3-keto-l-gulonate 6-phosphate decarboxylase 1kw1 
Crystal structure of 3-keto-l-gulonate 6-phosphate decarboxylase with bound l-gulonate 6-phosphate 1l2u 
Orotidine 5'-monophosphate decarboxylase from e. coli 1lol 
Crystal structure of orotidine monophosphate decarboxylase complex with xmp 1loq 
Crystal structure of orotidine monophosphate decarboxylase complexed with product ump 1lor 
Crystal structure of orotidine 5'-monophosphate complexed with bmp 1los 
Crystal structure of orotidine monophosphate decarboxylase mutant deltar203a complexed with 6-azaump 1lp6 
Crystal structure of orotidine monophosphate decarboxylase complexed with cmp 1q6l 
Structure of 3-keto-l-gulonate 6-phosphate decarboxylase with bound l-threonohydroxamate 4-phosphate 1q6o 
Structure of 3-keto-l-gulonate 6-phosphate decarboxylase with bound l-gulonaet 6-phosphate 1q6q 
Structure of 3-keto-l-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate 1q6r 
Structure of 3-keto-l-gulonate 6-phosphate decarboxylase with bound l-xylulose 5-phosphate 1so3 
Crystal structure of h136a mutant of 3-keto-l-gulonate 6- phosphate decarboxylase with bound l-threonohydroxamate 4- phosphate 1so4 
Crystal structure of k64a mutant of 3-keto-l-gulonate 6- phosphate decarboxylase with bound l-threonohydroxamate 4- phosphate 1so5 
Crystal structure of e112q mutant of 3-keto-l-gulonate 6- phosphate decarboxylase with bound l-threonohydroxamate 4- phosphate 1so6 
Crystal structure of e112q/h136a double mutant of 3-keto-l- gulonate 6-phosphate decarboxylase with bound l- threonohydroxamate 4-phosphate 1vqt 
Crystal structure of orotidine 5'-phosphate decarboxylase (tm0332) from thermotoga maritima at 2.00 a resolution 1x1z 
Orotidine 5'-monophosphate decarboxylase (odcase) complexed with bmp (produced from 6-cyanoump) 1xbv 
Crystal structure of 3-keto-l-gulonate 6-phosphate decarboxylase with bound d-ribulose 5-phosphate 1xbx 
Structure of 3-keto-l-gulonate 6-phosphate decarboxylase e112d/r139v/t169a mutant with bound d-ribulose 5-phosphate 1xby 
Structure of 3-keto-l-gulonate 6-phosphate decarboxylase e112d/t169a mutant with bound d-ribulose 5-phosphate 1xbz 
Crystal structure of 3-keto-l-gulonate 6-phosphate decarboxylase e112d/r139v/t169a mutant with bound l- xylulose 5-phosphate 2aqw 
Structure of putative orotidine-monophosphate-decarboxylase from plasmodium yoelii (py01515) 2cz5 
Crystal structure of orotidine 5'-phosphate decarboxylase from pyrococcus horikoshii ot3 2czd 
Crystal structure of orotidine 5'-phosphate decarboxylase from pyrococcus horikoshii ot3 at 1.6 a resolution 2cze 
Crystal structure of orotidine 5'-phosphate decarboxylase from pyrococcus horikoshii ot3 complexed with ump 2czf 
Crystal structure of orotidine 5'-phosphate decarboxylase from pyrococcus horikoshii ot3 complexed with xmp 2e6y 
Covalent complex of orotidine 5'-monophosphate decarboxylase (odcase) with 6-iodo-ump 2eaw 
Human ump synthase (c-terminal domain- orotidine 5'- monophosphate decarboxylase) 2f84 
Crystal structure of an orotidine-5'-monophosphate decarboxylase homolog from p.falciparum 2fds 
Crystal structure of plasmodium berghei orotidine 5'- monophosphate decarboxylase (ortholog of plasmodium falciparum pf10_0225) 2ffc 
Crystal structure of plasmodium vivax orotidine- monophosphate-decarboxyl ump bound 2guu 
Crystal structure of plasmodium vivax orotidine 5- monophosphate decarboxylase with 6-aza-ump bound 2jgy 
The crystal structure of human orotidine-5'-decarboxylase domain of human uridine monophosphate synthetase (umps) 2p1f 
Human ump synthase (c-terminal domain-orotidine 5'- monophosphate decarboxylase) 2q8l 
Crystal structure of orotidine 5'-phosphate decarboxylase from plasmodium falciparum 2q8z 
Crystal structure of plasmodium falciparum orotidine 5'- phosphate decarboxylase complexed with 6-amino-ump 2qaf 
Crystal structure of plasmodium falciparum orotidine 5'- phosphate decarboxylase covalently modified by 6-iodo-ump 2qcc 
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human ump synthase, apo form 2qcd 
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human ump synthase bound to ump 2qce 
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human ump synthase bound to sulfate, glycerol, and chloride 2qcf 
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (asp312asn mutant) of human ump synthase bound to 5-fluoro-ump 2qcg 
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human ump synthase bound to 5- bromo-ump 2qch 
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human ump synthase bound to 5-iodo- ump 2qcl 
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (asp312asn mutant) of human ump synthase bound to omp 2qcm 
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (asp312asn mutant) of human ump synthase bound to 6-hydroxymethyl-ump 2qcn 
Covalent complex of the orotidine-5'-monophosphate decarboxylase domain of human ump synthase with 6-iodo-ump 2v30 
Human orotidine 5'-phosphate decarboxylase domain of uridine monophospate synthetase (umps) in complex with its product ump. 2yyt 
Crystal structure of uncharacterized conserved protein from geobacillus kaustophilus 2yyu 
Crystal structure of uncharacterized conserved protein from geobacillus kaustophilus 2za1 
Crystal structure of orotidine 5'-monophosphate decarboxylase complexed with orotidine 5'-monophosphate from p.falciparum 2za2 
Crystal structure of the apo-form of orotidine-5'- monophosphate decarboxylase from p.falciparum 2za3 
Crystal structure of orotidine 5'-monophosphate decarboxylase complexed with uridine 5'-monophosphate from p.falciparum 2zcg 
Structure and inhibition of orotidine 5'-phosphate decarboxylase from plasmodium falciparum 2zz1 
Snapshot of the reaction from 6-cn-ump to bmp catalyzed by orotidine monophosphate deacarboxylase from m. thermoautotrophicum 2zz2 
Orotidine monophosphate decarboxylase k72a mutant from m. thermoautotrophicum complexed with 6-cyano-ump 2zz3 
Covalent complex of orotidine monophosphate decarboxylase d70a mutant from m. thermoautotrophicus with 6-cyano-ump 2zz4 
Covalent complex of orotidine monophosphate decarboxylase d75n mutant from m. thermoautotrophicum with 6-cyano-ump 2zz5 
Orotidine monophosphate deacarboxylase d70a/k72a double mutant from m. thermoautotrophicum complexed with 6- cyano- ump 2zz6 
Covalent complex of orotidine monophosphate decarboxylase from m. thermoautotrophicum with 6-azido-ump 2zz7 
Orotidine monophosphate decarboxylase k72a mutant complexed with bmp (produced from 6-iodo-ump) 3bar 
Crystal structure of plasmodium falciparum orotidine 5'- phosphate decarboxylase covalently modified by 6-azido-ump 3bgg 
Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with bmp 3bgj 
Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently modified by 6-iodo-ump 3bk0 
Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-cn-ump 3bpw 
Crystal structure of p. falciparum orotidine 5'- monophosphate decarboxylase complexed with xmp 3bvj 
Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with xmp 3dbp 
Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 6-nh2-ump 3ewu 
D312n mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-acetyl-ump, covalent adduct 3eww 
D312n mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-cyano-ump, covalent adduct 3ewx 
K314a mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-ump, degraded to bmp 3ewy 
K314a mutant of human orotidyl-5'-monophosphate decarboxylase soaked with omp, decarboxylated to ump 3ewz 
Human orotidyl-5'-monophosphate decarboxylase in complex with 5-cyano-ump 3ex0 
Human orotidyl-5'-monophosphate decarboxylase in complex with 6-acetyl-ump 3ex1 
Human orotidyl-5'-monophosphate decarboxylase soaked with 6- cyano-ump, converted to ump 3ex2 
Human orotidyl-5'-monophosphate decarboxylase in complex with 6-cyano-ump 3ex3 
Human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-ump, covalent adduct 3ex4 
Human orotidyl-5'-monophosphate decarboxylase in complex with bmp 3ex5 
Human orotidyl-5'-monophosphate decarboxylase in complex with 6-mercapto-ump 3ex6 
D312n mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-ump, covalent adduct 3exr 
Crystal structure of kgpdc from streptococcus mutans 3exs 
Crystal structure of kgpdc from streptococcus mutans in complex with d-r5p 3ext 
Crystal structure of kgpdc from streptococcus mutans 3f4w 
The 1.65a crystal structure of 3-hexulose-6-phosphate synthase from salmonella typhimurium 3g18 
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum 3g1a 
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate 3g1d 
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with uridine 5'-monophosphate 3g1f 
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 5,6-dihydroorotidine 5'-monophosphate 3g1h 
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate 3g1s 
Crystal structure of the mutant d70g of orotidine 5'- monophosphate decarboxylase from methanobacterium thermoautotrophicum 3g1v 
Crystal structure of the mutant d70g of orotidine 5'- monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 5-fluorouridine 5'- monophosphate 3g1x 
Crystal structure of the mutant d70g of orotidine 5'- monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with uridine 5'-monophosphate 3g1y 
Crystal structure of the mutant d70n of orotidine 5'- monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with sulfate 3g22 
Crystal structure of the mutant d70n of orotidine 5'- monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with uridine 5'-monophosphate 3g24 
Crystal structure of the mutant d70n of orotidine 5'- monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'- monophosphate 3g3d 
Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently modified by 5-fluoro-6-azido-ump 3g3m 
Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently modified by 5-fluoro-6-iodo-ump 3gdk 
Crystal structure of the orotidine 5'-monophosphate decarboxylase from saccharomyces cerevisiae 3gdl 
Crystal structure of the orotidine 5'-monophosphate decarboxylase from saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate 3gdr 
Crystal structure of the d91n mutant of the orotidine 5'- monophosphate decarboxylase from saccharomyces cerevisiae 3gdt 
Crystal structure of the d91n mutant of the orotidine 5'- monophosphate decarboxylase from saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate 3ieb 
Crystal structure of 3-keto-l-gulonate-6-phosphate decarboxylase from vibrio cholerae o1 biovar el tor str. n16961 3jr2 
X-ray crystal structure of the mg-bound 3-keto-l-gulonate-6- phosphate decarboxylase from vibrio cholerae o1 biovar el tor str. n16961 - Links (links to other resources describing this domain)
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PFAM OMPdecase INTERPRO IPR001754