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Protein

Phosphatase/phosphodiesterase DR_1281

Gene

DR_1281

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Has a dual activity phosphatase/phosphodiesterase in vitro, with a preference to phosphoenolpyruvate (PEP) and 2',3'-cAMP, respectively. Can also use 2',3'-cGMP, 2',3'-cCMP and various model substrates such as p-nitrophenyl phosphate (pNPP), bis-p-nitrophenyl phosphate (bis-pNPP) and p-nitrophenyl thymidine monophosphate (pNP-TMP).1 Publication

Catalytic activityi

Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate.1 Publication
Phosphoenolpyruvate + H2O = pyruvate + phosphate.1 Publication

Cofactori

Mn2+1 Publication, Co2+1 Publication, Fe2+1 PublicationNote: Mn2+ is the preferable metal for phosphatase activity. Phosphodiesterase activity is observed in the presence of Co2+, Mn2+ or Fe2+.1 Publication

Kineticsi

kcat is 0.18 sec(-1) with PEP as substrate. kcat is 0.38 sec(-1) with 2',3'-cAMP as substrate. kcat is 0.32 sec(-1) with 2',3'-cCMP as substrate. kcat is 0.42 sec(-1) with 2',3'-cGMP as substrate. kcat is 0.20 sec(-1) with pNPP as substrate. kcat is 6.97 sec(-1) with bis-pNPP as substrate. kcat is 1.41 sec(-1) with pNP-TMP as substrate.1 Publication
  1. KM=0.36 mM for PEP (at pH 6.5)1 Publication
  2. KM=0.55 mM for 2',3'-cAMP (at pH 6.5)1 Publication
  3. KM=0.87 mM for 2',3'-cCMP (at pH 6.5)1 Publication
  4. KM=1.28 mM for 2',3'-cGMP (at pH 6.5)1 Publication
  5. KM=0.08 mM for pNPP (at pH 8.5)1 Publication
  6. KM=0.22 mM for bis-pNPP (at pH 8.5)1 Publication
  7. KM=0.05 mM for pNP-TMP (at pH 8.5)1 Publication
  1. Vmax=0.38 µmol/min/mg enzyme with PEP as substrate (at pH 6.5)1 Publication
  2. Vmax=0.83 µmol/min/mg enzyme with 2',3'-cAMP as substrate (at pH 6.5)1 Publication
  3. Vmax=0.68 µmol/min/mg enzyme with 2',3'-cCMP as substrate (at pH 6.5)1 Publication
  4. Vmax=0.91 µmol/min/mg enzyme with 2',3'-cGMP as substrate (at pH 6.5)1 Publication
  5. Vmax=0.44 µmol/min/mg enzyme with pNPP as substrate (at pH 8.5)1 Publication
  6. Vmax=13.8 µmol/min/mg enzyme with bis-pNPP as substrate (at pH 8.5)1 Publication
  7. Vmax=2.79 µmol/min/mg enzyme with pNP-TMP as substrate (at pH 8.5)1 Publication

pH dependencei

Optimum pH is 6.0-7.0.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi8Divalent metal cation 1By similarity1
Metal bindingi37Divalent metal cation 1By similarity1
Metal bindingi37Divalent metal cation 2By similarity1
Metal bindingi38Divalent metal cation 1By similarity1
Metal bindingi65Divalent metal cation 2By similarity1
Active sitei66Proton donorBy similarity1
Metal bindingi148Divalent metal cation 2; via tele nitrogenBy similarity1
Metal bindingi173Divalent metal cation 2; via pros nitrogenBy similarity1
Metal bindingi175Divalent metal cation 1; via tele nitrogenBy similarity1

GO - Molecular functioni

Keywordsi

Molecular functionHydrolase
LigandCobalt, Iron, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciDRAD243230:GH46-1309-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphatase/phosphodiesterase DR_1281Curated
Alternative name(s):
2',3'-cyclic-nucleotide 2'-phosphodiesteraseCurated (EC:3.1.4.161 Publication)
Calcineurin-like phosphoesterase1 Publication
Phosphoenolpyruvate phosphataseCurated (EC:3.1.3.601 Publication)
Gene namesi
Ordered Locus Names:DR_1281Imported
OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Taxonomic identifieri243230 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus
Proteomesi
  • UP000002524 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004396401 – 255Phosphatase/phosphodiesterase DR_1281Add BLAST255

Interactioni

Protein-protein interaction databases

STRINGi243230.DR_1281.

Structurei

Secondary structure

1255
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 6Combined sources5
Helixi11 – 25Combined sources15
Helixi26 – 28Combined sources3
Beta strandi30 – 35Combined sources6
Turni39 – 42Combined sources4
Helixi47 – 56Combined sources10
Beta strandi59 – 62Combined sources4
Turni65 – 68Combined sources4
Helixi73 – 78Combined sources6
Beta strandi99 – 104Combined sources6
Beta strandi106 – 116Combined sources11
Helixi127 – 134Combined sources8
Beta strandi142 – 148Combined sources7
Helixi152 – 162Combined sources11
Beta strandi165 – 174Combined sources10
Beta strandi182 – 184Combined sources3
Turni185 – 187Combined sources3
Beta strandi188 – 192Combined sources5
Beta strandi197 – 203Combined sources7
Helixi209 – 217Combined sources9
Beta strandi230 – 240Combined sources11
Beta strandi243 – 253Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1T70X-ray2.30A/B/C/D/E/F/G/H1-255[»]
ProteinModelPortaliQ9RUV0.
SMRiQ9RUV0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RUV0.

Family & Domainsi

Sequence similaritiesi

Belongs to the YmdB-like family.Curated

Phylogenomic databases

eggNOGiENOG4105D48. Bacteria.
COG1692. LUCA.
HOGENOMiHOG000011009.
InParanoidiQ9RUV0.
KOiK09769.
OMAiDAGMTGP.
OrthoDBiPOG091H06UZ.

Family and domain databases

Gene3Di3.60.21.10. 1 hit.
InterProiView protein in InterPro
IPR029052. Metallo-depent_PP-like.
IPR005235. YmdB-like.
PANTHERiPTHR36303. PTHR36303. 1 hit.
PfamiView protein in Pfam
PF13277. YmdB. 1 hit.
PIRSFiPIRSF004789. DR1281. 1 hit.
SUPFAMiSSF56300. SSF56300. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9RUV0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRVLFIGDVF GQPGRRVLQN HLPTIRPQFD FVIVNMENSA GGFGMHRDAA
60 70 80 90 100
RGALEAGAGC LTLGNHAWHH KDIYPMLSED TYPIVRPLNY ADPGTPGVGW
110 120 130 140 150
RTFDVNGEKL TVVNLLGRVF MEAVDNPFRT MDALLERDDL GTVFVDFHAE
160 170 180 190 200
ATSEKEAMGW HLAGRVAAVI GTHTHVPTAD TRILKGGTAY QTDAGFTGPH
210 220 230 240 250
DSIIGSAIEG PLQRFLTERP HRYGVAEGRA ELNGVALHFE GGKATAAERY

RFIED
Length:255
Mass (Da):27,936
Last modified:May 1, 2000 - v1
Checksum:i82F9DB08AD169D46
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF10852.1.
PIRiD75415.
RefSeqiNP_295005.1. NC_001263.1.
WP_010887924.1. NZ_CP015081.1.

Genome annotation databases

EnsemblBacteriaiAAF10852; AAF10852; DR_1281.
GeneIDi1800415.
KEGGidra:DR_1281.
PATRICifig|243230.17.peg.1477.

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.

Entry informationi

Entry nameiPPDE_DEIRA
AccessioniPrimary (citable) accession number: Q9RUV0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 12, 2017
Last sequence update: May 1, 2000
Last modified: July 5, 2017
This is version 100 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, Reference proteome

Documents

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