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Q9R5V5

- NTD_LACLE

UniProt

Q9R5V5 - NTD_LACLE

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Protein
Nucleoside deoxyribosyltransferase
Gene
ntd
Organism
Lactobacillus leichmannii
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

Catalyzes the cleavage of the glycosidic bond of 2'-deoxyribonucleosides and the transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base.2 Publications

Catalytic activityi

2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1.1 Publication

pH dependencei

Optimum pH is 6.0.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei98 – 981Nucleophile1 Publication

GO - Molecular functioni

  1. deoxyribonucleoside 5'-monophosphate N-glycosidase activity Source: InterPro
  2. nucleoside deoxyribosyltransferase activity Source: UniProtKB-EC
Complete GO annotation...

GO - Biological processi

  1. deoxyribonucleoside monophosphate catabolic process Source: InterPro
  2. nucleotide salvage Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Nucleotide metabolism

Enzyme and pathway databases

UniPathwayiUPA00312.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside deoxyribosyltransferase (EC:2.4.2.6)
Short name:
N-deoxyribosyltransferase
Gene namesi
Name:ntd
OrganismiLactobacillus leichmannii
Taxonomic identifieri28039 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi98 – 981E → A: Loss of transferase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 157156Nucleoside deoxyribosyltransferase
PRO_0000220067Add
BLAST

Interactioni

Subunit structurei

Homohexamer.1 Publication

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 94
Helixi15 – 3016
Helixi36 – 383
Helixi42 – 443
Helixi47 – 493
Turni52 – 543
Helixi56 – 605
Helixi62 – 7716
Beta strandi79 – 857
Helixi88 – 903
Helixi93 – 10412
Beta strandi108 – 1136
Helixi115 – 1173
Helixi124 – 1296
Beta strandi131 – 1355
Helixi136 – 1383
Turni139 – 1413

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1F8XX-ray2.50A/B1-157[»]
1F8YX-ray2.40A/B1-157[»]
4HX9X-ray2.68A/B/C/D/E/F/G/H1-157[»]
ProteinModelPortaliQ9R5V5.
SMRiQ9R5V5. Positions 2-157.

Miscellaneous databases

EvolutionaryTraceiQ9R5V5.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di3.40.50.1810. 1 hit.
InterProiIPR007710. Nucleoside_deoxyribTrfase.
[Graphical view]
PfamiPF05014. Nuc_deoxyrib_tr. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9R5V5-1 [UniParc]FASTAAdd to Basket

« Hide

MPKKTIYFGA GWFTDRQNKA YKEAMEALKE NPTIDLENSY VPLDNQYKGI    50
RVDEHPEYLH DKVWATATYN NDLNGIKTND IMLGVYIPDE EDVGLGMELG 100
YALSQGKYVL LVIPDEDYGK PINLMSWGVS DNVIKMSQLK DFNFNKPRFD 150
FYEGAVY 157
Length:157
Mass (Da):18,080
Last modified:January 23, 2007 - v3
Checksum:iF3CA8CA6F509A91F
GO

Cross-referencesi

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1F8X X-ray 2.50 A/B 1-157 [» ]
1F8Y X-ray 2.40 A/B 1-157 [» ]
4HX9 X-ray 2.68 A/B/C/D/E/F/G/H 1-157 [» ]
ProteinModelPortali Q9R5V5.
SMRi Q9R5V5. Positions 2-157.
ModBasei Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00312 .

Miscellaneous databases

EvolutionaryTracei Q9R5V5.

Family and domain databases

Gene3Di 3.40.50.1810. 1 hit.
InterProi IPR007710. Nucleoside_deoxyribTrfase.
[Graphical view ]
Pfami PF05014. Nuc_deoxyrib_tr. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98."
    Porter D.J.T., Merrill B.M., Short S.A.
    J. Biol. Chem. 270:15551-15556(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-26, FUNCTION, ACTIVE SITE, MUTAGENESIS OF GLU-98.
  2. "Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site."
    Armstrong S.R., Cook W.J., Short S.A., Ealick S.E.
    Structure 4:97-107(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).

Entry informationi

Entry nameiNTD_LACLE
AccessioniPrimary (citable) accession number: Q9R5V5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 13, 2004
Last sequence update: January 23, 2007
Last modified: October 16, 2013
This is version 53 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally (1 Publication) thought to originate from E.coli.

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

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

External Data

Dasty 3

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