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O35820 (DNPH1_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 72. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
2'-deoxynucleoside 5'-phosphate N-hydrolase 1
EC=3.2.2.-
Alternative name(s):
Deoxyribonucleoside 5'-monophosphate N-glycosidase
c-Myc-responsive protein Rcl
Gene names
Name:Dnph1
Synonyms:Rcl
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length163 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases. Ref.2

Catalytic activity

A deoxyribonucleoside 5'-monophosphate + H20 = deoxyribose 5-monophosphate + a purine or pyrimidine base. Ref.2

Enzyme regulation

Inhibited by zinc ions. Competitive inhibition of dGMP hydrolysis by GMP and 6-methylthio-GMP. Ref.2

Subunit structure

Monomer and homodimer. Ref.2

Subcellular location

Cytoplasm By similarity. Nucleus Ref.1.

Tissue specificity

Highly expressed in heart, kidney, liver and spleen. Weakly expressed in lung and skeletal muscle. Ref.1

Induction

Up-regulated in response to c-Myc and by partial hepatectomy. Ref.1 Ref.2

Sequence similarities

Belongs to the 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 family.

Biophysicochemical properties

Kinetic parameters:

KM=48 µM for dGMP Ref.2

KM=250 µM for dAMP

KM=450 µM for dIMP

KM=4 mM for dCMP

KM=15.6 mM for dUMP

Vmax=0.09 µmol/min/mg enzyme toward dGMP

pH dependence:

Optimum pH is 6.0 with dGMP or dCMP as substrate.

Mass spectrometry

Molecular mass is 17649.54±0.92 Da from positions 2 - 163. Determined by ESI. Ref.2

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.2
Chain2 – 1631622'-deoxynucleoside 5'-phosphate N-hydrolase 1 HAMAP-Rule MF_03036
PRO_0000097202

Regions

Region13 – 197Substrate binding HAMAP-Rule MF_03036
Region117 – 1193Substrate binding; shared with homodimeric partner HAMAP-Rule MF_03036

Sites

Binding site281Substrate
Binding site931Substrate

Amino acid modifications

Modified residue171Phosphoserine By similarity
Modified residue1581Phosphoserine By similarity

Experimental info

Mutagenesis131Y → A: 100-fold decrease binding affinity for GMP as substrate. Ref.3
Mutagenesis931E → A: 100-fold increase in Km and 170-fold decrease in catalytic efficiency for dGMP as substrate. Ref.2 Ref.3

Secondary structure

1 ............................... 163
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O35820 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: C670D4213F96D883

FASTA16317,781
        10         20         30         40         50         60 
MAASGEQAPC SVYFCGSIRG GREDQALYAR IVSRLRRYGK VLTEHVADAE LEPLGEEAAG 

        70         80         90        100        110        120 
GDQFIHEQDL NWLQQADVVV AEVTQPSLGV GYELGRAVAL GKPILCLFRP QSGRVLSAMI 

       130        140        150        160 
RGAADGSRFQ VWDYAEGEVE TMLDRYFEAY LPQKTASSSH PSA

« Hide

References

[1]"Identification of putative c-Myc-responsive genes: characterization of rcl, a novel growth-related gene."
Lewis B.C., Shim H., Li Q., Wu C.S., Lee L.A., Maity A., Dang C.V.
Mol. Cell. Biol. 17:4967-4978(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION.
Tissue: Liver.
[2]"The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase."
Ghiorghi Y.K., Zeller K.I., Dang C.V., Kaminski P.A.
J. Biol. Chem. 282:8150-8156(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, HOMODIMERIZATION, CLEAVAGE OF INITIATOR METHIONINE, MUTAGENESIS OF GLU-93.
[3]"Solution structure of RCL, a novel 2'-deoxyribonucleoside 5'-monophosphate N-glycosidase."
Doddapaneni K., Mahler B., Pavlovicz R., Haushalter A., Yuan C., Wu Z.
J. Mol. Biol. 394:423-434(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR IN COMPLEX WITH GMP, MUTAGENESIS OF TYR-13 AND GLU-93.
[4]"Structural characterization of the mammalian deoxynucleotide N-hydrolase Rcl and its stabilizing interactions with two inhibitors."
Yang Y., Padilla A., Zhang C., Labesse G., Kaminski P.A.
J. Mol. Biol. 394:435-447(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR IN COMPLEX WITH GMP.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		U82591 mRNA. Translation: AAB95314.1.
IPIIPI00213058.
RefSeqNP_598209.1. NM_133525.1.
UniGeneRn.6997.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2KHZNMR-A/B1-163[»]
2KLHNMR-A/B11-151[»]
4FYHX-ray2.44A/B/C/D11-151[»]
4FYIX-ray1.96A/B/C/D11-151[»]
4FYKX-ray1.79A/B/C/D11-151[»]
ProteinModelPortalO35820.
ModBaseSearch...

Protein-protein interaction databases

STRING10116.ENSRNOP00000024815.

Proteomic databases

PRIDEO35820.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000024815; ENSRNOP00000024815; ENSRNOG00000018397.
GeneID171047.
KEGGrno:171047.
UCSCRGD:620382. rat.

Organism-specific databases

CTD10591.
RGD620382. Dnph1.

Phylogenomic databases

eggNOGNOG08389.
GeneTreeENSGT00390000001216.
HOGENOMHOG000015361.
HOVERGENHBG079123.
InParanoidO35820.
OMAVYFCGSI.
OrthoDBEOG4K9BDM.

Gene expression databases

GenevestigatorO35820.
GermOnlineENSRNOG00000018397. Rattus norvegicus.

Family and domain databases

HAMAPMF_03036. Nuc_phosphate_hydrolase.
InterProIPR007710. Nucleoside_deoxyribTrfase.
[Graphical view]
PfamPF05014. Nuc_deoxyrib_tr. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO35820.
NextBio621577.

Entry information

Entry nameDNPH1_RAT
AccessionPrimary (citable) accession number: O35820
Entry history
Integrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: January 1, 1998
Last modified: April 3, 2013
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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