UniProtKB - Q9RUV0 (PPDE_DEIRA)
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
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
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
- KM=0.36 mM for PEP (at pH 6.5)1 Publication
- KM=0.55 mM for 2',3'-cAMP (at pH 6.5)1 Publication
- KM=0.87 mM for 2',3'-cCMP (at pH 6.5)1 Publication
- KM=1.28 mM for 2',3'-cGMP (at pH 6.5)1 Publication
- KM=0.08 mM for pNPP (at pH 8.5)1 Publication
- KM=0.22 mM for bis-pNPP (at pH 8.5)1 Publication
- KM=0.05 mM for pNP-TMP (at pH 8.5)1 Publication
- Vmax=0.38 µmol/min/mg enzyme with PEP as substrate (at pH 6.5)1 Publication
- Vmax=0.83 µmol/min/mg enzyme with 2',3'-cAMP as substrate (at pH 6.5)1 Publication
- Vmax=0.68 µmol/min/mg enzyme with 2',3'-cCMP as substrate (at pH 6.5)1 Publication
- Vmax=0.91 µmol/min/mg enzyme with 2',3'-cGMP as substrate (at pH 6.5)1 Publication
- Vmax=0.44 µmol/min/mg enzyme with pNPP as substrate (at pH 8.5)1 Publication
- Vmax=13.8 µmol/min/mg enzyme with bis-pNPP as substrate (at pH 8.5)1 Publication
- 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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 8 | Divalent metal cation 1By similarity | 1 | |
Metal bindingi | 37 | Divalent metal cation 1By similarity | 1 | |
Metal bindingi | 37 | Divalent metal cation 2By similarity | 1 | |
Metal bindingi | 38 | Divalent metal cation 1By similarity | 1 | |
Metal bindingi | 65 | Divalent metal cation 2By similarity | 1 | |
Active sitei | 66 | Proton donorBy similarity | 1 | |
Metal bindingi | 148 | Divalent metal cation 2; via tele nitrogenBy similarity | 1 | |
Metal bindingi | 173 | Divalent metal cation 2; via pros nitrogenBy similarity | 1 | |
Metal bindingi | 175 | Divalent metal cation 1; via tele nitrogenBy similarity | 1 |
GO - Molecular functioni
- 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity Source: UniProtKB-EC
- 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity Source: GO_Central
- metal ion binding Source: UniProtKB-KW
- phosphoenolpyruvate phosphatase activity Source: UniProtKB-EC
Keywordsi
Molecular function | Hydrolase |
Ligand | Cobalt, Iron, Manganese, Metal-binding |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Ordered Locus Names:DR_1281Imported |
Organismi | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) |
Taxonomic identifieri | 243230 [NCBI] |
Taxonomic lineagei | Bacteria › Deinococcus-Thermus › Deinococci › Deinococcales › Deinococcaceae › Deinococcus › |
Proteomesi |
|
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000439640 | 1 – 255 | Phosphatase/phosphodiesterase DR_1281Add BLAST | 255 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | Q9RUV0 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q9RUV0 |
Family & Domainsi
Sequence similaritiesi
Belongs to the YmdB-like family.Curated
Phylogenomic databases
eggNOGi | COG1692, Bacteria |
HOGENOMi | CLU_068238_0_0_0 |
InParanoidi | Q9RUV0 |
OMAi | NHIWDKK |
OrthoDBi | 1127353at2 |
Family and domain databases
Gene3Di | 3.60.21.10, 1 hit |
InterProi | View protein in InterPro IPR029052, Metallo-depent_PP-like IPR005235, YmdB-like |
PANTHERi | PTHR36303, PTHR36303, 1 hit |
Pfami | View protein in Pfam PF13277, YmdB, 1 hit |
PIRSFi | PIRSF004789, DR1281, 1 hit |
i Sequence
Sequence statusi: Complete.
Q9RUV0-1 [UniParc]FASTAAdd to basket
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
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AE000513 Genomic DNA Translation: AAF10852.1 |
PIRi | D75415 |
RefSeqi | NP_295005.1, NC_001263.1 WP_010887924.1, NZ_CP015081.1 |
Genome annotation databases
EnsemblBacteriai | AAF10852; AAF10852; DR_1281 |
KEGGi | dra:DR_1281 |
PATRICi | fig|243230.17.peg.1477 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AE000513 Genomic DNA Translation: AAF10852.1 |
PIRi | D75415 |
RefSeqi | NP_295005.1, NC_001263.1 WP_010887924.1, NZ_CP015081.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1T70 | X-ray | 2.30 | A/B/C/D/E/F/G/H | 1-255 | [»] | |
SMRi | Q9RUV0 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
STRINGi | 243230.DR_1281 |
Genome annotation databases
EnsemblBacteriai | AAF10852; AAF10852; DR_1281 |
KEGGi | dra:DR_1281 |
PATRICi | fig|243230.17.peg.1477 |
Phylogenomic databases
eggNOGi | COG1692, Bacteria |
HOGENOMi | CLU_068238_0_0_0 |
InParanoidi | Q9RUV0 |
OMAi | NHIWDKK |
OrthoDBi | 1127353at2 |
Miscellaneous databases
EvolutionaryTracei | Q9RUV0 |
Family and domain databases
Gene3Di | 3.60.21.10, 1 hit |
InterProi | View protein in InterPro IPR029052, Metallo-depent_PP-like IPR005235, YmdB-like |
PANTHERi | PTHR36303, PTHR36303, 1 hit |
Pfami | View protein in Pfam PF13277, YmdB, 1 hit |
PIRSFi | PIRSF004789, DR1281, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | PPDE_DEIRA | |
Accessioni | Q9RUV0Primary (citable) accession number: Q9RUV0 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | April 12, 2017 |
Last sequence update: | May 1, 2000 | |
Last modified: | December 2, 2020 | |
This is version 110 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families