Q9R5V5 (NTD_LACLE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nucleoside deoxyribosyltransferase
Short name=N-deoxyribosyltransferase
EC=2.4.2.6

Gene names

Name:

ntd

Organism

Lactobacillus leichmannii

Taxonomic identifier

28039 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Lactobacillales › Lactobacillaceae › Lactobacillus

Protein attributes

Sequence length	157 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the cleavage of the glycosidic bond of 2'-deoxyribonucleosides and the transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base. Ref.1 Ref.2
Catalytic activity	2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1. Ref.1
Pathway	Nucleotide metabolism; nucleotide salvage pathway. Ref.1 Ref.2
Subunit structure	Homohexamer. Ref.2
Sequence similarities	Belongs to the nucleoside deoxyribosyltransferase family.
Caution	Was originally (Ref.1) thought to originate from E.coli.
Biophysicochemical properties	pH dependence: Optimum pH is 6.0.

Ontologies

Keywords
Biological process	Nucleotide metabolism
Molecular function	Transferase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	deoxyribonucleoside monophosphate catabolic process Inferred from electronic annotation. Source: InterPro nucleotide salvage Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	deoxyribonucleoside 5'-monophosphate N-glycosidase activity Inferred from electronic annotation. Source: InterPro nucleoside deoxyribosyltransferase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1

Chain

2 – 157

156

Nucleoside deoxyribosyltransferase

PRO_0000220067

Sites

Active site

98

1

Nucleophile Ref.1

Experimental info

Mutagenesis

98

1

E → A: Loss of transferase activity. Ref.1

Secondary structure

1

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157

Helix Strand Turn

Details...

Beta strand

6 – 9

4

Helix

15 – 30

16

Helix

36 – 38

3

Helix

42 – 44

3

Helix

47 – 49

3

Turn

52 – 54

3

Helix

56 – 60

5

Helix

62 – 77

16

Beta strand

79 – 85

7

Helix

88 – 90

3

Helix

93 – 104

12

Beta strand

108 – 113

6

Helix

115 – 117

3

Helix

124 – 129

6

Beta strand

131 – 135

5

Helix

136 – 138

3

Turn

139 – 141

3

Sequences

	Sequence		Length	Mass (Da)
	Q9R5V5 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: F3CA8CA6F509A91F	FASTA	157	18,080
	10 20 30 40 50 60 MPKKTIYFGA GWFTDRQNKA YKEAMEALKE NPTIDLENSY VPLDNQYKGI RVDEHPEYLH 70 80 90 100 110 120 DKVWATATYN NDLNGIKTND IMLGVYIPDE EDVGLGMELG YALSQGKYVL LVIPDEDYGK 130 140 150 PINLMSWGVS DNVIKMSQLK DFNFNKPRFD FYEGAVY

References

[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).

Cross-references

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q9R5V5.

SMR

Q9R5V5. Positions 2-157.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

UniPathway

UPA00312.

Family and domain databases

InterPro

IPR007710. Nucleoside_deoxyribTrfase.
[Graphical view]

Pfam

PF05014. Nuc_deoxyrib_tr. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9R5V5.

Entry information

Entry name

NTD_LACLE

Accession

Primary (citable) accession number: Q9R5V5

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 13, 2004
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 51 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program