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Protein

Nucleoside deoxyribosyltransferase

Gene

ntd

Organism
Lactobacillus leichmannii
Status
Reviewed-Annotation score: 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: nucleotide salvage pathway

This protein is involved in the pathway nucleotide salvage pathway, which is part of Nucleotide metabolism.
View all proteins of this organism that are known to be involved in the pathway nucleotide salvage pathway and in Nucleotide metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei98Nucleophile1 Publication1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Nucleotide metabolism

Enzyme and pathway databases

BRENDAi2.4.2.6. 2878.
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)DescriptionActionsGraphical viewLength
Mutagenesisi98E → A: Loss of transferase activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00002200672 – 157Nucleoside deoxyribosyltransferaseAdd BLAST156

Interactioni

Subunit structurei

Homohexamer.1 Publication

Structurei

Secondary structure

1157
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 9Combined sources4
Helixi15 – 30Combined sources16
Helixi36 – 38Combined sources3
Helixi42 – 44Combined sources3
Helixi47 – 49Combined sources3
Turni52 – 54Combined sources3
Helixi56 – 60Combined sources5
Helixi62 – 77Combined sources16
Beta strandi79 – 85Combined sources7
Helixi88 – 90Combined sources3
Helixi93 – 104Combined sources12
Beta strandi108 – 113Combined sources6
Helixi115 – 117Combined sources3
Helixi124 – 129Combined sources6
Beta strandi131 – 135Combined sources5
Helixi136 – 138Combined sources3
Turni139 – 141Combined sources3

3D structure databases

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

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00312.
BRENDAi2.4.2.6. 2878.

Miscellaneous databases

EvolutionaryTraceiQ9R5V5.

Family and domain databases

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

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: November 2, 2016
This is version 62 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.