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Protein

Dihydroorotate dehydrogenase A (fumarate)

Gene

pyrDA

Organism
Lactococcus lactis subsp. cremoris (strain MG1363)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro, but cannot use NAD+ as an electron acceptor.1 Publication

Catalytic activityi

(S)-dihydroorotate + fumarate = orotate + succinate.1 Publication

Cofactori

FMN2 PublicationsNote: Binds 1 FMN per subunit.2 Publications

Kineticsi

  1. KM=18 µM for dihydroorotate1 Publication
  2. KM=250 µM for fumarate1 Publication
  1. Vmax=18.6 µmol/min/mg enzyme1 Publication

Pathwayi: UMP biosynthesis via de novo pathway

This protein is involved in the pathway UMP biosynthesis via de novo pathway, which is part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the pathway UMP biosynthesis via de novo pathway and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei19FMN2 Publications1
Binding sitei43Substrate1
Binding sitei127FMN2 Publications1
Binding sitei127Substrate1
Active sitei130Nucleophile1
Binding sitei164FMN2 Publications1
Binding sitei192FMN; via carbonyl oxygen2 Publications1
Binding sitei221FMN; via amide nitrogen2 Publications1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi43 – 44FMN2 Publications2
Nucleotide bindingi249 – 250FMN2 Publications2
Nucleotide bindingi271 – 272FMN2 Publications2

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyrimidine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BRENDAi1.3.1.14. 2903.
UniPathwayiUPA00070.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydroorotate dehydrogenase A (fumarate) (EC:1.3.98.1)
Short name:
DHOD A
Short name:
DHODase A
Short name:
DHOdehase A
Gene namesi
Name:pyrDA
Ordered Locus Names:llmg_0952
OrganismiLactococcus lactis subsp. cremoris (strain MG1363)
Taxonomic identifieri416870 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeLactococcus
Proteomesi
  • UP000000364 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi43K → A: More than 500-fold reduction of enzymatic activity with oxygen or DCIP as electron acceptor. 1 Publication1
Mutagenesisi43K → E: 40-fold reduction of enzymatic activity with oxygen as electron acceptor; more than 120-fold reduction with DCIP as electron acceptor. 1 Publication1
Mutagenesisi50R → E: Steady state kinetics comparable to wild-type; 3-fold decrease in flavin bleaching rate. 1 Publication1
Mutagenesisi56P → A: More than 500-fold reduction of enzymatic activity. 1 Publication1
Mutagenesisi57R → A: More active than wild-type, especially with 2,6-dichloroindophenol as electron acceptor. 1 Publication1
Mutagenesisi67N → A: 100-fold lower affinity for dihydroorotate. 1 Publication1
Mutagenesisi127N → A: 70-fold lower affinity for dihydroorotate; inhibited by milimolar concentrations of fumarate. 1 Publication1
Mutagenesisi129S → A: 6-fold lower enzymatic activity with fumarate as electron acceptor. 1 Publication1
Mutagenesisi130C → A or S: Almost total loss of activity with oxygen or 2,6-dichloroindophenol as electron acceptor. 1 Publication1
Mutagenesisi131P → A: 4.5-fold lower enzymatic activity with fumarate and 2,6-dichloroindophenol as electron acceptor. 1 Publication1
Mutagenesisi132N → A: 54-fold reduction of enzymatic activity with oxygen as electron acceptor; more than 250-fold reduction with 2,6-dichloroindophenol as electron acceptor. 2 Publications1
Mutagenesisi136K → A: Slightly higher affinity to dihydroorotate; 2-fold decrease in flavin bleaching rate. 1 Publication1
Mutagenesisi164K → A: Almost total loss of activity with oxygen or 2,6-dichloroindophenol as electron acceptor. 1 Publication1
Mutagenesisi193N → A: 500-fold lower affinity for dihydroorotate; inhibited by milimolar concentrations of fumarate. 1 Publication1
Mutagenesisi213K → A: 7-fold decrease in enzymatic activity; 50-fold decrease in flavin bleaching rate. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002852391 – 311Dihydroorotate dehydrogenase A (fumarate)Add BLAST311

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

STRINGi416870.llmg_0952.

Structurei

Secondary structure

1311
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 6Combined sources3
Beta strandi9 – 17Combined sources9
Helixi26 – 34Combined sources9
Beta strandi58 – 61Combined sources4
Beta strandi64 – 67Combined sources4
Helixi76 – 89Combined sources14
Beta strandi92 – 94Combined sources3
Beta strandi97 – 100Combined sources4
Helixi105 – 117Combined sources13
Beta strandi122 – 128Combined sources7
Beta strandi133 – 135Combined sources3
Helixi139 – 141Combined sources3
Helixi143 – 153Combined sources11
Turni154 – 156Combined sources3
Beta strandi161 – 165Combined sources5
Helixi171 – 181Combined sources11
Beta strandi188 – 191Combined sources4
Beta strandi195 – 199Combined sources5
Turni203 – 206Combined sources4
Beta strandi207 – 209Combined sources3
Helixi212 – 215Combined sources4
Beta strandi216 – 221Combined sources6
Helixi222 – 224Combined sources3
Helixi225 – 236Combined sources12
Beta strandi243 – 250Combined sources8
Helixi254 – 263Combined sources10
Beta strandi266 – 270Combined sources5
Helixi272 – 277Combined sources6
Helixi281 – 296Combined sources16
Helixi301 – 303Combined sources3
Turni304 – 306Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DORX-ray2.00A/B1-311[»]
1JQVX-ray2.10A/B1-311[»]
1JQXX-ray1.70A/B1-311[»]
1JRBX-ray1.90A/B1-311[»]
1JRCX-ray1.80A/B1-311[»]
1JUBX-ray1.40A/B1-311[»]
1JUEX-ray1.80A/B1-311[»]
1NFCmodel-A1-311[»]
1OVDX-ray2.25A/B1-311[»]
2BSLX-ray2.30A/B1-311[»]
2BX7X-ray2.04A/B1-311[»]
2DORX-ray2.00A/B1-311[»]
ProteinModelPortaliA2RJT9.
SMRiA2RJT9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiA2RJT9.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni67 – 71Substrate binding5
Regioni193 – 194Substrate binding2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107RY0. Bacteria.
COG0167. LUCA.
HOGENOMiHOG000225104.
KOiK00226.
OMAiMAKKGYE.

Family and domain databases

CDDicd04741. DHOD_1A_like. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00224. DHO_dh_type1. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR033886. DHOD_1A.
IPR005720. Dihydroorotate_DH.
IPR024920. Dihydroorotate_DH_1.
IPR012135. Dihydroorotate_DH_1_2.
IPR001295. Dihydroorotate_DH_CS.
[Graphical view]
PfamiPF01180. DHO_dh. 1 hit.
[Graphical view]
PIRSFiPIRSF000164. DHO_oxidase. 1 hit.
TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
PROSITEiPS00911. DHODEHASE_1. 1 hit.
PS00912. DHODEHASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A2RJT9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLNTTFANAK FANPFMNASG VHCMTIEDLE ELKASQAGAY ITKSSTLEKR
60 70 80 90 100
EGNPLPRYVD LELGSINSMG LPNLGFDYYL DYVLKNQKEN AQEGPIFFSI
110 120 130 140 150
AGMSAAENIA MLKKIQESDF SGITELNLSC PNVPGKPQLA YDFEATEKLL
160 170 180 190 200
KEVFTFFTKP LGVKLPPYFD LVHFDIMAEI LNQFPLTYVN SVNSIGNGLF
210 220 230 240 250
IDPEAESVVI KPKDGFGGIG GAYIKPTALA NVRAFYTRLK PEIQIIGTGG
260 270 280 290 300
IETGQDAFEH LLCGATMLQI GTALHKEGPA IFDRIIKELE EIMNQKGYQS
310
IADFHGKLKS L
Length:311
Mass (Da):34,210
Last modified:March 6, 2007 - v1
Checksum:i30157E3C2791CDD7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X74206 Genomic DNA. Translation: CAA52279.1.
AM406671 Genomic DNA. Translation: CAL97544.1.
RefSeqiWP_011834894.1. NC_009004.1.

Genome annotation databases

EnsemblBacteriaiCAL97544; CAL97544; llmg_0952.
KEGGillm:llmg_0952.
PATRICi22283022. VBILacLac4574_0970.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X74206 Genomic DNA. Translation: CAA52279.1.
AM406671 Genomic DNA. Translation: CAL97544.1.
RefSeqiWP_011834894.1. NC_009004.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DORX-ray2.00A/B1-311[»]
1JQVX-ray2.10A/B1-311[»]
1JQXX-ray1.70A/B1-311[»]
1JRBX-ray1.90A/B1-311[»]
1JRCX-ray1.80A/B1-311[»]
1JUBX-ray1.40A/B1-311[»]
1JUEX-ray1.80A/B1-311[»]
1NFCmodel-A1-311[»]
1OVDX-ray2.25A/B1-311[»]
2BSLX-ray2.30A/B1-311[»]
2BX7X-ray2.04A/B1-311[»]
2DORX-ray2.00A/B1-311[»]
ProteinModelPortaliA2RJT9.
SMRiA2RJT9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi416870.llmg_0952.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL97544; CAL97544; llmg_0952.
KEGGillm:llmg_0952.
PATRICi22283022. VBILacLac4574_0970.

Phylogenomic databases

eggNOGiENOG4107RY0. Bacteria.
COG0167. LUCA.
HOGENOMiHOG000225104.
KOiK00226.
OMAiMAKKGYE.

Enzyme and pathway databases

UniPathwayiUPA00070.
BRENDAi1.3.1.14. 2903.

Miscellaneous databases

EvolutionaryTraceiA2RJT9.

Family and domain databases

CDDicd04741. DHOD_1A_like. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00224. DHO_dh_type1. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR033886. DHOD_1A.
IPR005720. Dihydroorotate_DH.
IPR024920. Dihydroorotate_DH_1.
IPR012135. Dihydroorotate_DH_1_2.
IPR001295. Dihydroorotate_DH_CS.
[Graphical view]
PfamiPF01180. DHO_dh. 1 hit.
[Graphical view]
PIRSFiPIRSF000164. DHO_oxidase. 1 hit.
TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
PROSITEiPS00911. DHODEHASE_1. 1 hit.
PS00912. DHODEHASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPYRDA_LACLM
AccessioniPrimary (citable) accession number: A2RJT9
Secondary accession number(s): P54321
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2007
Last sequence update: March 6, 2007
Last modified: November 30, 2016
This is version 69 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

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.