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Q9R5V5

- NTD_LACLE

UniProt

Q9R5V5 - NTD_LACLE

Protein

Nucleoside deoxyribosyltransferase

Gene

ntd

Organism
Lactobacillus leichmannii
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
  1. 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

    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 – 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.
    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

    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...
    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 1, 2014
    This is version 54 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