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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

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 leichmanniiCurated
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 deoxyribosyltransferasePRO_0000220067Add
BLAST

Interactioni

Subunit structurei

Homohexamer.1 Publication

Structurei

Secondary structure

1
157
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 94Combined sources
Helixi15 – 3016Combined sources
Helixi36 – 383Combined sources
Helixi42 – 443Combined sources
Helixi47 – 493Combined sources
Turni52 – 543Combined sources
Helixi56 – 605Combined sources
Helixi62 – 7716Combined sources
Beta strandi79 – 857Combined sources
Helixi88 – 903Combined sources
Helixi93 – 10412Combined sources
Beta strandi108 – 1136Combined sources
Helixi115 – 1173Combined sources
Helixi124 – 1296Combined sources
Beta strandi131 – 1355Combined sources
Helixi136 – 1383Combined sources
Turni139 – 1413Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

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

        10         20         30         40         50
MPKKTIYFGA GWFTDRQNKA YKEAMEALKE NPTIDLENSY VPLDNQYKGI
60 70 80 90 100
RVDEHPEYLH DKVWATATYN NDLNGIKTND IMLGVYIPDE EDVGLGMELG
110 120 130 140 150
YALSQGKYVL LVIPDEDYGK PINLMSWGVS DNVIKMSQLK DFNFNKPRFD

FYEGAVY
Length:157
Mass (Da):18,080
Last modified:January 23, 2007 - v3
Checksum:iF3CA8CA6F509A91F
GO

Cross-referencesi

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...
MobiDBi 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 29, 2014
This is version 55 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 thought to originate from E.coli.1 Publication

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