NRDD_BPT4
ID NRDD_BPT4 Reviewed; 605 AA.
AC P07071; P07073; Q38428; Q9T0V5;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2002, sequence version 4.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Anaerobic ribonucleoside-triphosphate reductase {ECO:0000305};
DE EC=1.1.98.6 {ECO:0000269|PubMed:8702830};
DE AltName: Full=Class III ribonucleoside-triphosphate reductase {ECO:0000305};
GN Name=nrdD {ECO:0000303|PubMed:8051113}; Synonyms=49.1, 55.11/55.13, SUNY;
OS Enterobacteria phage T4 (Bacteriophage T4).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Myoviridae; Tevenvirinae; Tequatrovirus.
OX NCBI_TaxID=10665;
OH NCBI_TaxID=562; Escherichia coli.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=C;
RX PubMed=3575111; DOI=10.1093/nar/15.8.3632;
RA Tomaschewski J., Rueger W.;
RT "Nucleotide sequence and primary structures of gene products coded for by
RT the T4 genome between map positions 48.266 kb and 39.166 kb.";
RL Nucleic Acids Res. 15:3632-3633(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=12626685; DOI=10.1128/mmbr.67.1.86-156.2003;
RA Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Ruger W.;
RT "Bacteriophage T4 genome.";
RL Microbiol. Mol. Biol. Rev. 67:86-156(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-181.
RX PubMed=2974005; DOI=10.1093/genetics/120.2.329;
RA Barth K.A., Powell D., Trupin M., Mosig G.;
RT "Regulation of two nested proteins from gene 49 (recombination endonuclease
RT VII) and of a lambda RexA-like protein of bacteriophage T4.";
RL Genetics 120:329-343(1988).
RN [4]
RP IDENTIFICATION.
RX PubMed=1938898; DOI=10.1128/jb.173.21.6980-6985.1991;
RA Zeh A., Shub D.A.;
RT "The product of the split sunY gene of bacteriophage T4 is a processed
RT protein.";
RL J. Bacteriol. 173:6980-6985(1991).
RN [5]
RP POSSIBLE FUNCTION.
RX PubMed=8421692; DOI=10.1073/pnas.90.2.577;
RA Sun X., Harder J., Krook M., Joernvall H., Sjoeberg B.-M., Reichard P.;
RT "A possible glycine radical in anaerobic ribonucleotide reductase from
RT Escherichia coli: nucleotide sequence of the cloned nrdD gene.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:577-581(1993).
RN [6]
RP FUNCTION AS AN ANAEROBIC RIBONUCLEOTIDE REDUCTASE.
RX PubMed=8051113; DOI=10.1016/s0021-9258(17)31980-4;
RA Young P., Oehman M., Xu M.Q., Shub D.A., Sjoeberg B.-M.;
RT "Intron-containing T4 bacteriophage gene sunY encodes an anaerobic
RT ribonucleotide reductase.";
RL J. Biol. Chem. 269:20229-20232(1994).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, SUBUNIT, INTERACTION
RP WITH NRDG, GLYCYL RADICAL AT GLY-580, AND MUTAGENESIS OF GLY-580.
RX PubMed=8702830; DOI=10.1074/jbc.271.34.20770;
RA Young P., Andersson J., Sahlin M., Sjoeberg B.-M.;
RT "Bacteriophage T4 anaerobic ribonucleotide reductase contains a stable
RT glycyl radical at position 580.";
RL J. Biol. Chem. 271:20770-20775(1996).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) OF MUTANT ALA-580.
RX PubMed=10066165; DOI=10.1126/science.283.5407.1499;
RA Logan D.T., Andersson J., Sjoeberg B.-M., Nordlund P.;
RT "A glycyl radical site in the crystal structure of a class III
RT ribonucleotide reductase.";
RL Science 283:1499-1504(1999).
RN [9] {ECO:0007744|PDB:1H78, ECO:0007744|PDB:1H79, ECO:0007744|PDB:1H7A, ECO:0007744|PDB:1H7B}
RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) IN COMPLEXES WITH DCTP; DTTP; DATP
RP AND IRON.
RX PubMed=11587648; DOI=10.1016/s0969-2126(01)00627-x;
RA Larsson K.M., Andersson J., Sjoberg B.M., Nordlund P., Logan D.T.;
RT "Structural basis for allosteric substrate specificity regulation in
RT anaerobic ribonucleotide reductases.";
RL Structure 9:739-750(2001).
RN [10] {ECO:0007744|PDB:1HK8}
RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) IN COMPLEX WITH DGTP AND ZINC, AND
RP ZINC-BINDING.
RX PubMed=12655046; DOI=10.1073/pnas.0736456100;
RA Logan D.T., Mulliez E., Larsson K.-M., Bodevin S., Atta M., Garnaud P.E.,
RA Sjoeberg B.-M., Fontecave M.;
RT "A metal-binding site in the catalytic subunit of anaerobic ribonucleotide
RT reductase.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:3826-3831(2003).
CC -!- FUNCTION: Catalyzes the conversion of ribonucleotides into
CC deoxyribonucleotides, which are required for DNA synthesis and repair.
CC {ECO:0000269|PubMed:8051113, ECO:0000269|PubMed:8702830}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + formate + H(+) = a 2'-
CC deoxyribonucleoside 5'-triphosphate + CO2 + H2O;
CC Xref=Rhea:RHEA:51476, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15740, ChEBI:CHEBI:16526, ChEBI:CHEBI:61557,
CC ChEBI:CHEBI:61560; EC=1.1.98.6;
CC Evidence={ECO:0000269|PubMed:8702830};
CC -!- ACTIVITY REGULATION: Activated under anaerobic conditions by NrdG, a
CC tightly associated activase. Activation involves the formation of a
CC glycyl radical at Gly-580. {ECO:0000269|PubMed:8702830}.
CC -!- SUBUNIT: Homodimer. Forms a tetramer composed of two NrdD and two NrdG
CC subunits. {ECO:0000269|PubMed:8702830}.
CC -!- SIMILARITY: Belongs to the anaerobic ribonucleoside-triphosphate
CC reductase family. {ECO:0000305}.
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DR EMBL; Y00122; CAA68308.1; -; Genomic_DNA.
DR EMBL; Y00122; CAA68310.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AF158101; AAD42633.1; -; Genomic_DNA.
DR EMBL; X12629; CAA31150.1; -; Genomic_DNA.
DR PIR; E29284; Z6BPT9.
DR PIR; S01907; Z4BPT9.
DR RefSeq; NP_049690.1; NC_000866.4.
DR PDB; 1H78; X-ray; 2.50 A; A=1-605.
DR PDB; 1H79; X-ray; 2.90 A; A=1-605.
DR PDB; 1H7A; X-ray; 2.75 A; A=1-605.
DR PDB; 1H7B; X-ray; 2.45 A; A=1-605.
DR PDB; 1HK8; X-ray; 2.45 A; A=1-605.
DR PDBsum; 1H78; -.
DR PDBsum; 1H79; -.
DR PDBsum; 1H7A; -.
DR PDBsum; 1H7B; -.
DR PDBsum; 1HK8; -.
DR SMR; P07071; -.
DR DrugBank; DB03258; 2'-Deoxycytidine 5'-triphosphate.
DR DrugBank; DB02181; 2'-Deoxyguanosine-5'-Triphosphate.
DR DrugBank; DB03222; dATP.
DR DrugBank; DB02452; Thymidine 5'-triphosphate.
DR GeneID; 1258655; -.
DR KEGG; vg:1258655; -.
DR BRENDA; 1.1.98.6; 732.
DR EvolutionaryTrace; P07071; -.
DR PRO; PR:P07071; -.
DR Proteomes; UP000009087; Genome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008998; F:ribonucleoside-triphosphate reductase activity; IEA:InterPro.
DR GO; GO:0006260; P:DNA replication; IEA:InterPro.
DR CDD; cd01675; RNR_III; 1.
DR InterPro; IPR019777; Form_AcTrfase_GR_CS.
DR InterPro; IPR001150; Gly_radical.
DR InterPro; IPR012833; NrdD.
DR Pfam; PF13597; NRDD; 1.
DR TIGRFAMs; TIGR02487; NrdD; 1.
DR PROSITE; PS00850; GLY_RADICAL_1; 1.
DR PROSITE; PS51149; GLY_RADICAL_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Metal-binding; Organic radical; Oxidoreductase;
KW Reference proteome; Zinc.
FT CHAIN 1..605
FT /note="Anaerobic ribonucleoside-triphosphate reductase"
FT /id="PRO_0000166686"
FT DOMAIN 482..605
FT /note="Glycine radical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00493"
FT BINDING 64
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H78"
FT BINDING 64
FT /ligand="dGTP"
FT /ligand_id="ChEBI:CHEBI:61429"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0007744|PDB:1HK8"
FT BINDING 66
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H78"
FT BINDING 66
FT /ligand="dGTP"
FT /ligand_id="ChEBI:CHEBI:61429"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0007744|PDB:1HK8"
FT BINDING 67
FT /ligand="dGTP"
FT /ligand_id="ChEBI:CHEBI:61429"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0007744|PDB:1HK8"
FT BINDING 100
FT /ligand="dATP"
FT /ligand_id="ChEBI:CHEBI:61404"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H7A"
FT BINDING 100
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H78"
FT BINDING 100
FT /ligand="dGTP"
FT /ligand_id="ChEBI:CHEBI:61429"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0007744|PDB:1HK8"
FT BINDING 100
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H79"
FT BINDING 103
FT /ligand="dATP"
FT /ligand_id="ChEBI:CHEBI:61404"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H7A"
FT BINDING 103
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H78"
FT BINDING 103
FT /ligand="dGTP"
FT /ligand_id="ChEBI:CHEBI:61429"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0007744|PDB:1HK8"
FT BINDING 114
FT /ligand="dATP"
FT /ligand_id="ChEBI:CHEBI:61404"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H7A"
FT BINDING 114
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H78"
FT BINDING 114
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H79"
FT BINDING 146
FT /ligand="dATP"
FT /ligand_id="ChEBI:CHEBI:61404"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H7A"
FT BINDING 146
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H78"
FT BINDING 146
FT /ligand="dGTP"
FT /ligand_id="ChEBI:CHEBI:61429"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0007744|PDB:1HK8"
FT BINDING 146
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H79"
FT BINDING 445..448
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:11587648,
FT ECO:0007744|PDB:1H78"
FT BINDING 447
FT /ligand="dGTP"
FT /ligand_id="ChEBI:CHEBI:61429"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0007744|PDB:1HK8"
FT BINDING 448
FT /ligand="dGTP"
FT /ligand_id="ChEBI:CHEBI:61429"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0007744|PDB:1HK8"
FT BINDING 543
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0000305|PubMed:11587648, ECO:0007744|PDB:1HK8"
FT BINDING 546
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0000305|PubMed:11587648, ECO:0007744|PDB:1HK8"
FT BINDING 561
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0000305|PubMed:11587648, ECO:0007744|PDB:1HK8"
FT BINDING 564
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:12655046,
FT ECO:0000305|PubMed:11587648, ECO:0007744|PDB:1HK8"
FT MOD_RES 580
FT /note="Glycine radical"
FT /evidence="ECO:0000269|PubMed:8702830"
FT MUTAGEN 580
FT /note="G->A: Lacks both glycyl radical and activity. Does
FT not affect interaction with NrdG."
FT /evidence="ECO:0000269|PubMed:8702830"
FT HELIX 30..47
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 52..59
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 62..65
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 66..73
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 84..89
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 105..120
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 123..125
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 132..148
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 149..155
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 159..184
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 185..188
FT /evidence="ECO:0007829|PDB:1H79"
FT STRAND 195..199
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 205..220
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 223..226
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 232..238
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 240..243
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 251..264
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 268..271
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 272..279
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 310..318
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 319..324
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 334..358
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 359..361
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 364..366
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 368..371
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 384..386
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 387..390
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 391..394
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 395..402
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 404..411
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 416..434
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 437..441
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 448..460
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 464..467
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 468..471
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 480..482
FT /evidence="ECO:0007829|PDB:1H78"
FT HELIX 486..493
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 494..498
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 506..509
FT /evidence="ECO:0007829|PDB:1H7B"
FT HELIX 517..530
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 532..537
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 540..542
FT /evidence="ECO:0007829|PDB:1H7B"
FT TURN 544..546
FT /evidence="ECO:0007829|PDB:1HK8"
FT STRAND 553..555
FT /evidence="ECO:0007829|PDB:1H7A"
FT STRAND 556..560
FT /evidence="ECO:0007829|PDB:1HK8"
FT STRAND 562..564
FT /evidence="ECO:0007829|PDB:1HK8"
FT HELIX 569..571
FT /evidence="ECO:0007829|PDB:1HK8"
FT STRAND 573..576
FT /evidence="ECO:0007829|PDB:1H7B"
FT STRAND 578..581
FT /evidence="ECO:0007829|PDB:1H7B"
SQ SEQUENCE 605 AA; 67957 MW; C5F29CE03126800B CRC64;
MTIEKEIEGL IHKTNKDLLN ENANKDSRVF PTQRDLMAGI VSKHIAKNMV PSFIMKAHES
GIIHVHDIDY SPALPFTNCC LVDLKGMLEN GFKLGNAQIE TPKSIGVATA IMAQITAQVA
SHQYGGTTFA NVDKVLSPYV KRTYAKHIED AEKWQIADAL NYAQSKTEKD VYDAFQAYEY
EVNTLFSSNG QTPFVTITFG TGTDWTERMI QKAILKNRIK GLGRDGITPI FPKLVMFVEE
GVNLYKDDPN YDIKQLALEC ASKRMYPDII SAKNNKAITG SSVPVSPMGC RSFLSVWKDS
TGNEILDGRN NLGVVTLNLP RIALDSYIGT QFNEQKFVEL FNERMDLCFE ALMCRISSLK
GVKATVAPIL YQEGAFGVRL KPDDDIIELF KNGRSSVSLG YIGIHELNIL VGRDIGREIL
TKMNAHLKQW TERTGFAFSL YSTPAENLCY RFCKLDTEKY GSVKDVTDKG WYTNSFHVSV
EENITPFEKI SREAPYHFIA TGGHISYVEL PDMKNNLKGL EAVWDYAAQH LDYFGVNMPV
DKCFTCGSTH EMTPTENGFV CSICGETDPK KMNTIRRTCG YLGNPNERGF NLGKNKEIMH
RVKHQ
