5'-nucleotidase yfbR - Escherichia coli (strain K12)

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P76491 (YFBR_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 97. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
5'-nucleotidase yfbR
EC=3.1.3.5

Alternative name(s):
5'-deoxyribonucleotidase
Nucleoside 5'-monophosphate phosphohydrolase

Gene names

Name:	yfbR
Ordered Locus Names:	b2291, JW2288

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	199 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Nucleotidase that shows strict specificity toward deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. Might be involved in the regulation of all dNTP pools in E.coli. Ref.3
Catalytic activity	A 5'-ribonucleotide + H₂O = a ribonucleoside + phosphate. HAMAP MF_01100
Cofactor	A divalent metal cation. Highest activity with cobalt, followed by manganese and Cu²⁺. Ref.3
Enzyme regulation	Inhibited by both ribo- and deoxyribonucleoside di- and triphosphates. HAMAP MF_01100
Subunit structure	Homooligomer in solution. The oligomeric complexes consist of three and more subunits. Ref.3
Subcellular location	Cytoplasm Potential HAMAP MF_01100.
Sequence similarities	Belongs to the UPF0207 family.
Biophysicochemical properties	Kinetic parameters: K_M=0.012 mM for 5'-dAMP Ref.3 K_M=0.047 mM for 5'-dGMP K_M=0.008 mM for 5'-dTMP K_M=0.020 mM for 5'-dUMP K_M=0.017 mM for 5'-dIMP K_M=0.036 mM for 5'-dCMP K_M=2.09 mM for pNPP V_max=0.71 µmol/min/mg enzyme with 5'-dAMP as substrate V_max=0.46 µmol/min/mg enzyme with 5'-dGMP as substrate V_max=0.37 µmol/min/mg enzyme with 5'-dTMP as substrate V_max=0.54 µmol/min/mg enzyme with 5'-dUMP as substrate V_max=0.56 µmol/min/mg enzyme with 5'-dIMP as substrate V_max=0.53 µmol/min/mg enzyme with 5'-dCMP as substrate V_max=1.32 µmol/min/mg enzyme with pNPP as substrate pH dependence: Optimum pH is 8.0.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Cobalt Copper Manganese Metal-binding Nucleotide-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	dUMP biosynthetic process Inferred from mutant phenotype. Source: EcoCyc
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	5'-nucleotidase activity Inferred from electronic annotation. Source: EC cobalt ion binding Inferred from direct assay Ref.3. Source: EcoCyc nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW phosphoric diester hydrolase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 199

199

5'-nucleotidase yfbR HAMAP MF_01100

PRO_0000095049

Secondary structure

199

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P76491 [UniParc].

Last modified February 1, 1997. Version 1.
Checksum: 895E9A06130DA057
Show »

FASTA

199

22,708

        10         20         30         40         50         60 
MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR KFGGNVNAER 

        70         80         90        100        110        120 
IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA QQKLVDMVPE ELRDIFAPLI 

       130        140        150        160        170        180 
DEHAYSDEEK SLVKQADALC AYLKCLEELA AGNNEFLLAK TRLEATLEAR RSQEMDYFME 

       190 
IFVPSFHLSL DEISQDSPL

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG." Proudfoot M., Kuznetsova E., Brown G., Rao N.N., Kitagawa M., Mori H., Savchenko A., Yakunin A.F. J. Biol. Chem. 279:54687-54694(2004) [PubMed: 15489502] [Abstract] Cited for: FUNCTION, CHARACTERIZATION, COFACTOR, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
[4]	"Structure of Apc11001: hypothetical member of the HD metal-binding phosphohydrolase superfamily." Zimmerman M.D., Chruszcz M., Cymborowski M.T., Kudritska M., Spencer J., Minor W. Submitted (OCT-2004) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00096 Genomic DNA. Translation: AAC75351.1.
AP009048 Genomic DNA. Translation: BAE76684.1.

PIR

A65001.

RefSeq

NP_416794.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2PAQ	X-ray	2.10	A/B	1-199	[»]
2PAR	X-ray	2.10	A/B	1-199	[»]
2PAU	X-ray	2.10	A/B	1-199	[»]

ProteinModelPortal

P76491.

SMR

P76491. Positions 2-187.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-28107N.

IntAct

P76491. 2 interactions.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000000958; EBESCP00000000958; EBESCG00000000787.
EBESCT00000017678; EBESCP00000016969; EBESCG00000016734.

GeneID

946771.

GenomeReviews

Gene locus JW2288 in contig AP009048_GR.
Gene locus b2291 in contig U00096_GR.

KEGG

ecj:JW2288.
eco:b2291.

PATRIC

32119951. VBIEscCol129921_2385.

Organism-specific databases

EchoBASE

EB3855.

EcoGene

EG14102. yfbR.

Phylogenomic databases

eggNOG

COG1896.

GeneTree

EBGT00050000010736.

HOGENOM

HBG298349.

OMA

QIAHEYK.

PhylomeDB

P76491.

ProtClustDB

PRK03826.

Enzyme and pathway databases

BioCyc

EcoCyc:G7185-MONOMER.
MetaCyc:G7185-MONOMER.

BRENDA

3.1.3.5. 2026.

Gene expression databases

Genevestigator

P76491.

Family and domain databases

HAMAP

MF_01100. UPF0207.
[Tree]

InterPro

IPR022971. dCMP_phosphohydrolase.
IPR023279. HD.
IPR003607. Metal-dep_PHydrolase_HD_dom.
IPR006674. Metal-dep_PHydrolase_HD_sub.
[Graphical view]

Gene3D

G3DSA:1.10.3210.10. HD. 1 hit.

K08722.

Pfam

PF01966. HD. 1 hit.
[Graphical view]

SMART

SM00471. HDc. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

YFBR_ECOLI

Accession

Primary (citable) accession number: P76491
Secondary accession number(s): Q2MAM2

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 27, 2002
Last sequence update:	February 1, 1997
Last modified:	January 25, 2012
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Uncharacterized protein families (UPF)

List of uncharacterized protein family (UPF) entries

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents