ID   NTD_LACLE               Reviewed;         157 AA.
AC   Q9R5V5;
DT   13-SEP-2004, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 3.
DT   03-MAY-2023, entry version 75.
DE   RecName: Full=Nucleoside deoxyribosyltransferase;
DE            Short=N-deoxyribosyltransferase;
DE            EC=2.4.2.6;
GN   Name=ntd;
OS   Lactobacillus leichmannii.
OC   Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae;
OC   Lactobacillus.
OX   NCBI_TaxID=28039 {ECO:0000305};
RN   [1] {ECO:0000305}
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-26, FUNCTION,
RP   ACTIVE SITE, AND MUTAGENESIS OF GLU-98.
RX   PubMed=7797550; DOI=10.1074/jbc.270.26.15551;
RA   Porter D.J.T., Merrill B.M., Short S.A.;
RT   "Identification of the active site nucleophile in nucleoside 2-
RT   deoxyribosyltransferase as glutamic acid 98.";
RL   J. Biol. Chem. 270:15551-15556(1995).
RN   [2] {ECO:0000305}
RP   X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
RX   PubMed=8805514; DOI=10.1016/s0969-2126(96)00013-5;
RA   Armstrong S.R., Cook W.J., Short S.A., Ealick S.E.;
RT   "Crystal structures of nucleoside 2-deoxyribosyltransferase in native and
RT   ligand-bound forms reveal architecture of the active site.";
RL   Structure 4:97-107(1996).
CC   -!- FUNCTION: Catalyzes the cleavage of the glycosidic bond of 2'-
CC       deoxyribonucleosides and the transfer of the deoxyribosyl moiety to an
CC       acceptor purine or pyrimidine base. {ECO:0000269|PubMed:7797550,
CC       ECO:0000269|PubMed:8805514}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2-deoxy-D-ribosyl-base(1) + base(2) = 2-deoxy-D-ribosyl-
CC         base(2) + base(1).; EC=2.4.2.6;
CC         Evidence={ECO:0000269|PubMed:7797550};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 6.0.;
CC   -!- PATHWAY: Nucleotide metabolism; nucleotide salvage pathway.
CC   -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:8805514}.
CC   -!- SIMILARITY: Belongs to the nucleoside deoxyribosyltransferase family.
CC       {ECO:0000305}.
CC   -!- CAUTION: Was originally thought to originate from E.coli.
CC       {ECO:0000305|PubMed:7797550}.
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DR   RefSeq; WP_035184009.1; NZ_QOCY01000049.1.
DR   PDB; 1F8X; X-ray; 2.50 A; A/B=1-157.
DR   PDB; 1F8Y; X-ray; 2.40 A; A/B=1-157.
DR   PDB; 4HX9; X-ray; 2.68 A; A/B/C/D/E/F/G/H=1-157.
DR   PDBsum; 1F8X; -.
DR   PDBsum; 1F8Y; -.
DR   PDBsum; 4HX9; -.
DR   AlphaFoldDB; Q9R5V5; -.
DR   SMR; Q9R5V5; -.
DR   DrugBank; DB03763; 5-methyl-2'-deoxypseudouridine.
DR   BRENDA; 2.4.2.6; 2878.
DR   UniPathway; UPA00312; -.
DR   EvolutionaryTrace; Q9R5V5; -.
DR   GO; GO:0050144; F:nucleoside deoxyribosyltransferase activity; IEA:UniProtKB-EC.
DR   GO; GO:0043173; P:nucleotide salvage; IEA:UniProtKB-UniPathway.
DR   Gene3D; 3.40.50.450; -; 1.
DR   InterPro; IPR007710; Nucleoside_deoxyribTrfase.
DR   Pfam; PF05014; Nuc_deoxyrib_tr; 1.
DR   SUPFAM; SSF52309; N-(deoxy)ribosyltransferase-like; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Direct protein sequencing; Nucleotide metabolism;
KW   Transferase.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000269|PubMed:7797550"
FT   CHAIN           2..157
FT                   /note="Nucleoside deoxyribosyltransferase"
FT                   /id="PRO_0000220067"
FT   ACT_SITE        98
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000269|PubMed:7797550"
FT   MUTAGEN         98
FT                   /note="E->A: Loss of transferase activity."
FT                   /evidence="ECO:0000269|PubMed:7797550"
FT   STRAND          6..9
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           15..30
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           36..38
FT                   /evidence="ECO:0007829|PDB:1F8X"
FT   HELIX           42..44
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           47..49
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   TURN            52..54
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           56..60
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           62..77
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   STRAND          79..85
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           88..90
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           93..104
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   STRAND          108..113
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           115..117
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           124..129
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   STRAND          131..135
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   HELIX           136..138
FT                   /evidence="ECO:0007829|PDB:1F8Y"
FT   TURN            139..141
FT                   /evidence="ECO:0007829|PDB:1F8Y"
SQ   SEQUENCE   157 AA;  18080 MW;  F3CA8CA6F509A91F CRC64;
     MPKKTIYFGA GWFTDRQNKA YKEAMEALKE NPTIDLENSY VPLDNQYKGI RVDEHPEYLH
     DKVWATATYN NDLNGIKTND IMLGVYIPDE EDVGLGMELG YALSQGKYVL LVIPDEDYGK
     PINLMSWGVS DNVIKMSQLK DFNFNKPRFD FYEGAVY
//