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 08-NOV-2023, entry version 140. 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}; GN Synonyms=49.1, 55.11/55.13, SUNY; OS Enterobacteria phage T4 (Bacteriophage T4). OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; OC Straboviridae; 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 OrthoDB; 420at10239; -. DR BRENDA; 1.1.98.6; 732. DR EvolutionaryTrace; P07071; -. DR PRO; PR:P07071; -. DR Proteomes; UP000009087; Segment. 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 Gene3D; 3.20.70.20; -; 1. DR InterPro; IPR019777; Form_AcTrfase_GR_CS. DR InterPro; IPR001150; Gly_radical. DR InterPro; IPR012833; NrdD. DR NCBIfam; TIGR02487; NrdD; 1. DR PANTHER; PTHR21075; ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE; 1. DR PANTHER; PTHR21075:SF0; ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE; 1. DR Pfam; PF13597; NRDD; 1. DR SUPFAM; SSF51998; PFL-like glycyl radical enzymes; 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 //