UniProtKB - P0AF24 (NAGD_ECOLI)
Protein
Ribonucleotide monophosphatase NagD
Gene
nagD
Organism
Escherichia coli (strain K12)
Status
Functioni
Catalyzes the dephosphorylation of an unusually broad range of substrate including deoxyribo- and ribonucleoside tri-, di-, and monophosphates, as well as polyphosphate and glucose-1-P (Glu1P).2 Publications
Catalytic activityi
- EC:3.1.3.51 Publication
Cofactori
Mg2+2 Publications, Mn2+2 Publications, Co2+2 Publications, Zn2+2 PublicationsNote: Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.2 Publications
Kineticsi
- KM=160 µM for UMP (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=400 µM for GMP (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=840 µM for AMP (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=840 µM for ribose-5-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=1470 µM for CMP (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=1500 µM for dTMP (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=1500 µM for pyridoxal 5-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=1700 µM for glycerol 3-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=5900 µM for glucose 6-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=6000 µM for glucosamine 6-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=6000 µM for dCMP (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=6500 µM for dAMP (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=7600 µM for dGMP (at pH 7 and at 25 degrees Celsius)1 Publication
- KM=7700 µM for dGMP (at pH 7 and at 25 degrees Celsius)1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 9 | Nucleophile1 Publication | 1 | |
Metal bindingi | 9 | MagnesiumCombined sources1 Publication | 1 | |
Active sitei | 11 | Proton donor/acceptor1 Publication | 1 | |
Metal bindingi | 11 | Magnesium; via carbonyl oxygenCombined sources1 Publication | 1 | |
Binding sitei | 11 | Substrate | 1 | |
Sitei | 55 | Orients D-11 for proton transfer during catalytic turnover1 Publication | 1 | |
Sitei | 146 | Confers substrate specificity | 1 | |
Binding sitei | 176 | Substrate | 1 | |
Metal bindingi | 201 | MagnesiumCombined sources1 Publication | 1 |
GO - Molecular functioni
- 5'-nucleotidase activity Source: UniProtKB
- magnesium ion binding Source: UniProtKB
- phosphatase activity Source: GO_Central
GO - Biological processi
- carbohydrate metabolic process Source: UniProtKB-KW
- UMP catabolic process Source: EcoCyc
Keywordsi
Molecular function | Hydrolase |
Biological process | Carbohydrate metabolism |
Ligand | Magnesium, Metal-binding |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10634-MONOMER ECOL316407:JW0661-MONOMER MetaCyc:EG10634-MONOMER |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:nagD Ordered Locus Names:b0675, JW0661 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000096694 | 1 – 250 | Ribonucleotide monophosphatase NagDAdd BLAST | 250 |
Proteomic databases
EPDi | P0AF24 |
jPOSTi | P0AF24 |
PaxDbi | P0AF24 |
PRIDEi | P0AF24 |
Expressioni
Inductioni
By N-acetylglucosamine.Curated
Interactioni
Subunit structurei
Monomer.
1 PublicationProtein-protein interaction databases
BioGridi | 4259613, 11 interactors |
DIPi | DIP-6861N |
IntActi | P0AF24, 4 interactors |
STRINGi | 511145.b0675 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P0AF24 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P0AF24 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 42 – 43 | Substrate binding | 2 | |
Regioni | 202 – 205 | Substrate binding | 4 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | ENOG4105D4U Bacteria COG0647 LUCA |
HOGENOMi | HOG000068105 |
InParanoidi | P0AF24 |
KOi | K02566 |
PhylomeDBi | P0AF24 |
Family and domain databases
Gene3Di | 3.40.50.1000, 2 hits |
InterProi | View protein in InterPro IPR036412 HAD-like_sf IPR006357 HAD-SF_hydro_IIA IPR023214 HAD_sf |
Pfami | View protein in Pfam PF13344 Hydrolase_6, 1 hit |
SUPFAMi | SSF56784 SSF56784, 1 hit |
TIGRFAMsi | TIGR01460 HAD-SF-IIA, 1 hit |
i Sequence
Sequence statusi: Complete.
P0AF24-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MTIKNVICDI DGVLMHDNVA VPGAAEFLHG IMDKGLPLVL LTNYPSQTGQ
60 70 80 90 100
DLANRFATAG VDVPDSVFYT SAMATADFLR RQEGKKAYVV GEGALIHELY
110 120 130 140 150
KAGFTITDVN PDFVIVGETR SYNWDMMHKA AYFVANGARF IATNPDTHGR
160 170 180 190 200
GFYPACGALC AGIEKISGRK PFYVGKPSPW IIRAALNKMQ AHSEETVIVG
210 220 230 240 250
DNLRTDILAG FQAGLETILV LSGVSSLDDI DSMPFRPSWI YPSVAEIDVI
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 97 | H → Y in AAC09327 (PubMed:2190615).Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X14135 Genomic DNA Translation: CAA32355.1 AF052007 Genomic DNA Translation: AAC09327.1 U00096 Genomic DNA Translation: AAC73769.1 AP009048 Genomic DNA Translation: BAA35318.1 |
PIRi | B64802 |
RefSeqi | NP_415201.1, NC_000913.3 WP_000153129.1, NZ_STEB01000044.1 WP_000153136.1, NZ_CP014272.1 |
Genome annotation databases
EnsemblBacteriai | AAC73769; AAC73769; b0675 BAA35318; BAA35318; BAA35318 |
GeneIDi | 945283 |
KEGGi | ecj:JW0661 eco:b0675 |
PATRICi | fig|511145.12.peg.700 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X14135 Genomic DNA Translation: CAA32355.1 AF052007 Genomic DNA Translation: AAC09327.1 U00096 Genomic DNA Translation: AAC73769.1 AP009048 Genomic DNA Translation: BAA35318.1 |
PIRi | B64802 |
RefSeqi | NP_415201.1, NC_000913.3 WP_000153129.1, NZ_STEB01000044.1 WP_000153136.1, NZ_CP014272.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2C4N | X-ray | 1.80 | A | 1-250 | [»] | |
SMRi | P0AF24 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGridi | 4259613, 11 interactors |
DIPi | DIP-6861N |
IntActi | P0AF24, 4 interactors |
STRINGi | 511145.b0675 |
Proteomic databases
EPDi | P0AF24 |
jPOSTi | P0AF24 |
PaxDbi | P0AF24 |
PRIDEi | P0AF24 |
Genome annotation databases
EnsemblBacteriai | AAC73769; AAC73769; b0675 BAA35318; BAA35318; BAA35318 |
GeneIDi | 945283 |
KEGGi | ecj:JW0661 eco:b0675 |
PATRICi | fig|511145.12.peg.700 |
Organism-specific databases
EchoBASEi | EB0628 |
Phylogenomic databases
eggNOGi | ENOG4105D4U Bacteria COG0647 LUCA |
HOGENOMi | HOG000068105 |
InParanoidi | P0AF24 |
KOi | K02566 |
PhylomeDBi | P0AF24 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10634-MONOMER ECOL316407:JW0661-MONOMER MetaCyc:EG10634-MONOMER |
Miscellaneous databases
EvolutionaryTracei | P0AF24 |
PROi | PR:P0AF24 |
Family and domain databases
Gene3Di | 3.40.50.1000, 2 hits |
InterProi | View protein in InterPro IPR036412 HAD-like_sf IPR006357 HAD-SF_hydro_IIA IPR023214 HAD_sf |
Pfami | View protein in Pfam PF13344 Hydrolase_6, 1 hit |
SUPFAMi | SSF56784 SSF56784, 1 hit |
TIGRFAMsi | TIGR01460 HAD-SF-IIA, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | NAGD_ECOLI | |
Accessioni | P0AF24Primary (citable) accession number: P0AF24 Secondary accession number(s): P15302 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | December 20, 2005 |
Last sequence update: | December 20, 2005 | |
Last modified: | November 13, 2019 | |
This is version 112 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, Complete proteome, Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families - Escherichia coli
Escherichia coli (strain K12): entries and cross-references to EcoGene - PDB cross-references
Index of Protein Data Bank (PDB) cross-references