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Protein

dCTP deaminase, dUMP-forming

Gene

dcd

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Bifunctional enzyme that catalyzes both the deamination of dCTP to dUTP and the hydrolysis of dUTP to dUMP without releasing the toxic dUTP intermediate. It also acts as a dUTP diphosphatase with a lower affinity for dUTP than for dCTP.2 Publications

Catalytic activityi

dCTP + 2 H2O = dUMP + diphosphate + NH3.UniRule annotation2 Publications

Cofactori

Mg2+2 Publications

Enzyme regulationi

Inhibited by dTTP.1 Publication

Kineticsi

  1. KM=17.6 µM for dCTP (at 60 degrees Celsius)1 Publication
  2. KM=263 µM for dUTP (at 60 degrees Celsius)1 Publication
  1. Vmax=14.7 µmol/min/mg enzyme with dCTP as substrate (at 60 degrees Celsius)1 Publication
  2. Vmax=23.9 µmol/min/mg enzyme with dUTP as substrate (at 60 degrees Celsius)1 Publication

pH dependencei

Optimum pH is 7.5.1 Publication

Temperature dependencei

Retains over 70% of its activity after heating at 90 degrees Celsius for 10 min.1 Publication

Pathwayi: dUMP biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes dUMP from dCTP.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. dCTP deaminase, dUMP-forming (dcd)
This subpathway is part of the pathway dUMP biosynthesis, which is itself part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes dUMP from dCTP, the pathway dUMP biosynthesis and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei128dCTP1 Publication1
Sitei132 – 133Important for bifunctional activityUniRule annotation2
Binding sitei132dCTP; via amide nitrogen1 Publication1
Binding sitei135dCTP; via amide nitrogenUniRule annotation1 Publication1
Active sitei145Proton donor/acceptorUniRule annotationBy similarity1
Binding sitei163dCTPUniRule annotation1
Binding sitei177dCTPUniRule annotation1 Publication1
Binding sitei184dCTPUniRule annotation1 Publication1
Binding sitei188dCTPUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi117 – 122dCTP bindingUniRule annotation6
Nucleotide bindingi143 – 145dCTP bindingUniRule annotation2 Publications3

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processNucleotide metabolism
LigandMagnesium, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-17894
MJAN243232:G1GKE-460-MONOMER
BRENDAi3.5.4.13 3260
3.5.4.30 3260
3.6.1.23 3260
SABIO-RKiQ57872
UniPathwayiUPA00610; UER00667

Protein family/group databases

MoonProtiQ57872

Names & Taxonomyi

Protein namesi
Recommended name:
dCTP deaminase, dUMP-formingUniRule annotationCurated (EC:3.5.4.30UniRule annotation2 Publications)
Alternative name(s):
Bifunctional dCTP deaminase:dUTPaseUniRule annotationCurated
DCD-DUT1 PublicationUniRule annotation
MjDCD-DUT1 Publication
Gene namesi
Name:dcdUniRule annotation
Ordered Locus Names:MJ0430
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi135D → N: Loss of activity. 1 Publication1
Mutagenesisi145E → Q: Loss of dCTP deaminase activity, but retains 25% dUTP pyrophosphatase activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001560291 – 204dCTP deaminase, dUMP-formingAdd BLAST204

Interactioni

Subunit structurei

Homotrimer (PubMed:12756253, PubMed:12909016). Two trimers assemble into a hexamer by stacking on top of each other (PubMed:12909016).2 Publications

Protein-protein interaction databases

STRINGi243232.MJ_0430

Structurei

Secondary structure

1204
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 13Combined sources9
Beta strandi16 – 21Combined sources6
Helixi24 – 26Combined sources3
Beta strandi32 – 36Combined sources5
Beta strandi38 – 43Combined sources6
Beta strandi45 – 47Combined sources3
Beta strandi56 – 60Combined sources5
Beta strandi62 – 68Combined sources7
Helixi76 – 86Combined sources11
Beta strandi89 – 94Combined sources6
Beta strandi96 – 105Combined sources10
Beta strandi110 – 116Combined sources7
Helixi118 – 121Combined sources4
Turni122 – 124Combined sources3
Beta strandi125 – 127Combined sources3
Beta strandi139 – 151Combined sources13
Beta strandi153 – 156Combined sources4
Beta strandi160 – 168Combined sources9
Beta strandi176 – 180Combined sources5
Helixi196 – 198Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OGHX-ray1.88A/B1-204[»]
1PKHX-ray1.42A/B1-204[»]
1PKJX-ray2.10A/B1-204[»]
1PKKX-ray1.77A/B1-204[»]
2HXBX-ray2.55A1-204[»]
2HXDX-ray2.30A1-204[»]
3GF0X-ray2.62A1-204[»]
ProteinModelPortaliQ57872
SMRiQ57872
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ57872

Family & Domainsi

Sequence similaritiesi

Belongs to the dCTP deaminase family.UniRule annotationCurated

Phylogenomic databases

eggNOGiarCOG04048 Archaea
COG0717 LUCA
InParanoidiQ57872
KOiK09887
OMAiGWIDAGF
OrthoDBiPOG093Z0C6C
PhylomeDBiQ57872

Family and domain databases

CDDicd07557 trimeric_dUTPase, 1 hit
Gene3Di2.70.40.10, 1 hit
HAMAPiMF_00146 dCTP_deaminase, 1 hit
InterProiView protein in InterPro
IPR011962 dCTP_deaminase
IPR029054 dUTPase-like
IPR036157 dUTPase-like_sf
IPR033704 dUTPase_trimeric
PfamiView protein in Pfam
PF00692 dUTPase, 1 hit
SUPFAMiSSF51283 SSF51283, 1 hit
TIGRFAMsiTIGR02274 dCTP_deam, 1 hit

Sequencei

Sequence statusi: Complete.

Q57872-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILSDKDIID YVTSKRIIIK PFNKDFVGPC SYDVTLGDEF IIYDDEVYDL
60 70 80 90 100
SKELNYKRIK IKNSILVCPL NYNLTEEKIN YFKEKYNVDY VVEGGVLGTT
110 120 130 140 150
NEYIELPNDI SAQYQGRSSL GRVFLTSHQT AGWIDAGFKG KITLEIVAFD
160 170 180 190 200
KPVILYKNQR IGQLIFSKLL SPADVGYSER KTSKYAYQKS VMPSLIHLDN

HKKD
Length:204
Mass (Da):23,432
Last modified:November 1, 1996 - v1
Checksum:i1218368057723371
GO

Mass spectrometryi

Molecular mass is 23619±94 Da from positions 1 - 204. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA Translation: AAB98415.1
PIRiF64353
RefSeqiWP_010869929.1, NC_000909.1

Genome annotation databases

EnsemblBacteriaiAAB98415; AAB98415; MJ_0430
GeneIDi1451290
KEGGimja:MJ_0430

Similar proteinsi

Entry informationi

Entry nameiDCDB_METJA
AccessioniPrimary (citable) accession number: Q57872
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: April 25, 2018
This is version 135 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health