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Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small subunit)

 D3YPA4_HHV1             Unreviewed;       340 AA.
D3YPA4;
20-APR-2010, integrated into UniProtKB/TrEMBL.
20-APR-2010, sequence version 1.
28-FEB-2018, entry version 40.
RecName: Full=Ribonucleoside-diphosphate reductase small subunit {ECO:0000256|HAMAP-Rule:MF_04028};
EC=1.17.4.1 {ECO:0000256|HAMAP-Rule:MF_04028};
AltName: Full=Ribonucleotide reductase small subunit {ECO:0000256|HAMAP-Rule:MF_04028};
Name=UL40 {ECO:0000313|EMBL:ADD60039.1};
Synonyms=RIR2 {ECO:0000256|HAMAP-Rule:MF_04028};
ORFNames=HHV1gp058 {ECO:0000313|EMBL:AFE62868.1};
Human herpesvirus 1 (HHV-1) (Human herpes simplex virus 1).
Viruses; dsDNA viruses, no RNA stage; Herpesvirales; Herpesviridae;
Alphaherpesvirinae; Simplexvirus.
NCBI_TaxID=10298 {ECO:0000313|EMBL:ADD60039.1, ECO:0000313|Proteomes:UP000121444};
NCBI_TaxID=9606; Homo sapiens (Human).
[1] {ECO:0000313|EMBL:ADD60039.1, ECO:0000313|Proteomes:UP000121444}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=F {ECO:0000313|EMBL:ADD60039.1};
PubMed=20219902; DOI=10.1128/JVI.00312-10;
Szpara M.L., Parsons L., Enquist L.W.;
"Sequence variability in clinical and laboratory isolates of herpes
simplex virus 1 reveals new mutations.";
J. Virol. 84:5303-5313(2010).
[2] {ECO:0000313|EMBL:ADM23283.1}
NUCLEOTIDE SEQUENCE.
STRAIN=CR38 {ECO:0000313|EMBL:ADM23283.1},
R11 {ECO:0000313|EMBL:ADM23729.1}, R62 {ECO:0000313|EMBL:ADM23805.1},
S23 {ECO:0000313|EMBL:ADM23579.1}, and
S25 {ECO:0000313|EMBL:ADM23654.1};
PubMed=22417106; DOI=10.1111/j.1749-6632.2011.06358.x;
Davison A.J.;
"Evolution of sexually transmitted and sexually transmissible human
herpesviruses.";
Ann. N. Y. Acad. Sci. 1230:E37-E49(2011).
[3] {ECO:0000313|EMBL:AER37763.1}
NUCLEOTIDE SEQUENCE.
STRAIN=CJ311 {ECO:0000313|EMBL:AER37763.1}, and
CJ970 {ECO:0000313|EMBL:AER37977.1};
PubMed=22016062; DOI=10.1167/iovs.11-7812;
Kolb A.W., Adams M., Cabot E.L., Craven M., Brandt C.R.;
"Multiplex sequencing of seven ocular herpes simplex virus type-1
genomes: phylogeny, sequence variability, and SNP distribution.";
Invest. Ophthalmol. Vis. Sci. 52:9061-9073(2011).
[4] {ECO:0000313|EMBL:AFE62868.1, ECO:0000313|Proteomes:UP000180972}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=KOS {ECO:0000313|EMBL:AFE62868.1};
PubMed=22570244; DOI=10.1128/JVI.00646-12;
Macdonald S.J., Mostafa H.H., Morrison L.A., Davido D.J.;
"Genome Sequence of Herpes Simplex Virus 1 Strain KOS.";
J. Virol. 86:6371-6372(2012).
[5] {ECO:0000313|EMBL:AFI23631.1, ECO:0000313|Proteomes:UP000107500}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=KOS {ECO:0000313|EMBL:AFI23631.1};
Payne K.M., Russell D.A., Kinchington P.R.;
"Complete genome sequence of Herpes Simplex Virus Type-1 strain KOS.";
Submitted (MAR-2012) to the EMBL/GenBank/DDBJ databases.
[6] {ECO:0000313|EMBL:ADM23283.1}
NUCLEOTIDE SEQUENCE.
STRAIN=CR38 {ECO:0000313|EMBL:ADM23283.1},
R11 {ECO:0000313|EMBL:ADM23729.1}, R62 {ECO:0000313|EMBL:ADM23805.1},
S23 {ECO:0000313|EMBL:ADM23579.1}, and
S25 {ECO:0000313|EMBL:ADM23654.1};
Davison A.J.;
Submitted (OCT-2013) to the EMBL/GenBank/DDBJ databases.
[7] {ECO:0000313|EMBL:AJE59985.1}
NUCLEOTIDE SEQUENCE.
STRAIN=F {ECO:0000313|EMBL:AJE60198.1},
H166syn {ECO:0000313|EMBL:AJE60414.1}, and
KOS {ECO:0000313|EMBL:AJE59985.1};
PubMed=25827418;
Parsons L.R., Tafuri Y.R., Shreve J.T., Bowen C.D., Shipley M.M.,
Enquist L.W., Szpara M.L.;
"Rapid genome assembly and comparison decode intrastrain variation in
human alphaherpesviruses.";
MBio 6:e02213-14(2015).
[8] {ECO:0000313|EMBL:ALO18637.1, ECO:0000313|Proteomes:UP000110586, ECO:0000313|Proteomes:UP000180950}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=KOS {ECO:0000313|EMBL:ALO18637.1}, and
KOS 1.1 {ECO:0000313|EMBL:ALO18713.1};
PubMed=26547038; DOI=10.1016/j.virol.2015.09.026;
Colgrove R.C., Liu X., Griffiths A., Raja P., Deluca N.A.,
Newman R.M., Coen D.M., Knipe D.M.;
"History and genomic sequence analysis of the herpes simplex virus 1
KOS and KOS1.1 sub-strains.";
Virology 487:215-221(2015).
[9] {ECO:0000313|EMBL:ALM22831.1}
NUCLEOTIDE SEQUENCE.
STRAIN=KOS63 {ECO:0000313|EMBL:ALM22831.1};
Bowen C.D., Renner D.W., Shreve J.T., Tafuri Y., Payne K.M., Dix R.D.,
Gatherer D., Kinchington P., Szpara M.L.;
"Genetic Distance in Herpes Simplex Virus Isolates of the Same
Lineage.";
Submitted (AUG-2015) to the EMBL/GenBank/DDBJ databases.
[10] {ECO:0000313|EMBL:ALM22683.1}
NUCLEOTIDE SEQUENCE.
STRAIN=RDH193 {ECO:0000313|EMBL:ALM22683.1};
Sharkey C.M., Shreve J.T., Renner D.W., Szpara M.L.;
"Sequenced Genome of Herpes Simplex Virus 1 Encephalitic Clinical
Isolate H193.";
Submitted (AUG-2015) to the EMBL/GenBank/DDBJ databases.
[11] {ECO:0000313|EMBL:ARB08931.1}
NUCLEOTIDE SEQUENCE.
STRAIN=ZW6 {ECO:0000313|EMBL:ARB08931.1};
Chen C., Zhihua L., Yuzhong L., Yadong L., Yanwei B., Wei C.;
"Genomic sequence of a low passage herpes simplex type 1 clinical
strain ZW6.";
Submitted (JUN-2016) to the EMBL/GenBank/DDBJ databases.
[12] {ECO:0000313|EMBL:SBS69337.1}
NUCLEOTIDE SEQUENCE.
STRAIN=1319/2005 {ECO:0000313|EMBL:SBS69525.1},
172/2010 {ECO:0000313|EMBL:SBS69337.1},
3083/2008 {ECO:0000313|EMBL:SBS69405.1},
369/2007 {ECO:0000313|EMBL:SBS69427.1}, and
66/2007 {ECO:0000313|EMBL:SBS69605.1};
Kjaerup R.B., Dalgaard T.S., Juul-Madsen H.R.;
Submitted (JUN-2016) to the EMBL/GenBank/DDBJ databases.
[13] {ECO:0000313|EMBL:ASM47867.1}
NUCLEOTIDE SEQUENCE.
STRAIN=K {ECO:0000313|EMBL:ASM47867.1};
PubMed=28928148;
Oldfield L.M., Grzesik P., Voorhies A.A., Alperovich N., MacMath D.,
Najera C.D., Chandra D.S., Prasad S., Noskov V.N., Montague M.G.,
Friedman R.M., Desai P.J., Vashee S.;
"Genome-wide engineering of an infectious clone of herpes simplex
virus type 1 using synthetic genomics assembly methods.";
Proc. Natl. Acad. Sci. U.S.A. 114:E8885-E8894(2017).
[14] {ECO:0000313|EMBL:ATD84726.1}
NUCLEOTIDE SEQUENCE.
STRAIN=HSV-N-7 {ECO:0000313|EMBL:ATD84803.1}, and
HSV-R-13 {ECO:0000313|EMBL:ATD84726.1};
Pandey U., Renner D.W., Thompson R., Szpara M.L., Sawtell N.;
"Father-to-son transmission of herpes simplex virus results in near-
perfect preservation of viral genome identity and in vitro
phenotypes.";
Submitted (APR-2017) to the EMBL/GenBank/DDBJ databases.
[15] {ECO:0000313|EMBL:ASM47867.1}
NUCLEOTIDE SEQUENCE.
STRAIN=K {ECO:0000313|EMBL:ASM47867.1};
Song R., Chenine A.L., Ruprecht R.M.;
Submitted (MAY-2017) to the EMBL/GenBank/DDBJ databases.
-!- FUNCTION: Ribonucleoside-diphosphate reductase holoenzyme provides
the precursors necessary for viral DNA synthesis. Allows virus
growth in non-dividing cells, as well as reactivation from latency
in infected hosts. Catalyzes the biosynthesis of
deoxyribonucleotides from the corresponding ribonucleotides.
{ECO:0000256|HAMAP-Rule:MF_04028}.
-!- CATALYTIC ACTIVITY: 2'-deoxyribonucleoside diphosphate +
thioredoxin disulfide + H(2)O = ribonucleoside diphosphate +
thioredoxin. {ECO:0000256|HAMAP-Rule:MF_04028}.
-!- COFACTOR:
Name=Fe cation; Xref=ChEBI:CHEBI:24875;
Evidence={ECO:0000256|HAMAP-Rule:MF_04028};
-!- PATHWAY: Genetic information processing; DNA replication.
{ECO:0000256|HAMAP-Rule:MF_04028}.
-!- SUBUNIT: Heterotetramer composed of a homodimer of the large
subunit (R1) and a homodimer of the small subunit (R2). Larger
multisubunit protein complex are also active, composed of
(R1)n(R2)n. {ECO:0000256|HAMAP-Rule:MF_04028}.
-!- SUBCELLULAR LOCATION: Host membrane {ECO:0000256|HAMAP-
Rule:MF_04028}; Single-pass membrane protein {ECO:0000256|HAMAP-
Rule:MF_04028}.
-!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase
small chain family. {ECO:0000256|HAMAP-Rule:MF_04028}.
-----------------------------------------------------------------------
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EMBL; GU734771; ADD60039.1; -; Genomic_DNA.
EMBL; HM585508; ADM23283.1; -; Genomic_DNA.
EMBL; HM585512; ADM23579.1; -; Genomic_DNA.
EMBL; HM585513; ADM23654.1; -; Genomic_DNA.
EMBL; HM585514; ADM23729.1; -; Genomic_DNA.
EMBL; HM585515; ADM23805.1; -; Genomic_DNA.
EMBL; JN420338; AER37763.1; -; Genomic_DNA.
EMBL; JN420341; AER37977.1; -; Genomic_DNA.
EMBL; JQ673480; AFE62868.1; -; Genomic_DNA.
EMBL; JQ780693; AFI23631.1; -; Genomic_DNA.
EMBL; KM222721; AJE59985.1; -; Genomic_DNA.
EMBL; KM222722; AJE60056.1; -; Genomic_DNA.
EMBL; KM222723; AJE60127.1; -; Genomic_DNA.
EMBL; KM222724; AJE60198.1; -; Genomic_DNA.
EMBL; KM222725; AJE60271.1; -; Genomic_DNA.
EMBL; KM222727; AJE60414.1; -; Genomic_DNA.
EMBL; KT425108; ALM22683.1; -; Genomic_DNA.
EMBL; KT425110; ALM22831.1; -; Genomic_DNA.
EMBL; KT899744; ALO18637.1; -; Genomic_DNA.
EMBL; KT887224; ALO18713.1; -; Genomic_DNA.
EMBL; KX424525; ARB08931.1; -; Genomic_DNA.
EMBL; MF156584; ASM47867.1; -; Genomic_DNA.
EMBL; KY922718; ATD84726.1; -; Genomic_DNA.
EMBL; KY922719; ATD84803.1; -; Genomic_DNA.
EMBL; LT594105; SBS69337.1; -; Genomic_DNA.
EMBL; LT594107; SBS69405.1; -; Genomic_DNA.
EMBL; LT594112; SBS69427.1; -; Genomic_DNA.
EMBL; LT594108; SBS69525.1; -; Genomic_DNA.
EMBL; LT594110; SBS69605.1; -; Genomic_DNA.
UniPathway; UPA00326; -.
Proteomes; UP000107500; Genome.
Proteomes; UP000110586; Genome.
Proteomes; UP000121444; Genome.
Proteomes; UP000180950; Genome.
Proteomes; UP000180972; Genome.
GO; GO:0033644; C:host cell membrane; IEA:UniProtKB-SubCell.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-UniRule.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IEA:UniProtKB-UniRule.
GO; GO:0009186; P:deoxyribonucleoside diphosphate metabolic process; IEA:UniProtKB-UniRule.
GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IEA:InterPro.
GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniRule.
CDD; cd01049; RNRR2; 1.
Gene3D; 1.10.620.20; -; 1.
HAMAP; MF_04028; HSV_RIR2; 1.
InterPro; IPR009078; Ferritin-like_SF.
InterPro; IPR034715; HSV_RIR2.
InterPro; IPR012348; RNR-like.
InterPro; IPR033909; RNR_small.
InterPro; IPR030475; RNR_small_AS.
InterPro; IPR000358; RNR_small_fam.
PANTHER; PTHR23409; PTHR23409; 1.
Pfam; PF00268; Ribonuc_red_sm; 1.
SUPFAM; SSF47240; SSF47240; 1.
PROSITE; PS00368; RIBORED_SMALL; 1.
3: Inferred from homology;
Complete proteome {ECO:0000313|Proteomes:UP000107500,
ECO:0000313|Proteomes:UP000110586, ECO:0000313|Proteomes:UP000121444,
ECO:0000313|Proteomes:UP000180950};
DNA replication {ECO:0000256|HAMAP-Rule:MF_04028};
Host membrane {ECO:0000256|HAMAP-Rule:MF_04028};
Iron {ECO:0000256|HAMAP-Rule:MF_04028};
Membrane {ECO:0000256|HAMAP-Rule:MF_04028};
Metal-binding {ECO:0000256|HAMAP-Rule:MF_04028};
Oxidoreductase {ECO:0000256|HAMAP-Rule:MF_04028,
ECO:0000313|EMBL:ADM23283.1};
Transmembrane {ECO:0000256|HAMAP-Rule:MF_04028};
Transmembrane helix {ECO:0000256|HAMAP-Rule:MF_04028}.
TRANSMEM 180 201 Helical. {ECO:0000256|HAMAP-
Rule:MF_04028}.
ACT_SITE 131 131 {ECO:0000256|HAMAP-Rule:MF_04028}.
METAL 94 94 Iron 1. {ECO:0000256|HAMAP-
Rule:MF_04028}.
METAL 124 124 Iron 1. {ECO:0000256|HAMAP-
Rule:MF_04028}.
METAL 124 124 Iron 2. {ECO:0000256|HAMAP-
Rule:MF_04028}.
METAL 127 127 Iron 1. {ECO:0000256|HAMAP-
Rule:MF_04028}.
METAL 187 187 Iron 2. {ECO:0000256|HAMAP-
Rule:MF_04028}.
METAL 221 221 Iron 2. {ECO:0000256|HAMAP-
Rule:MF_04028}.
METAL 224 224 Iron 2. {ECO:0000256|HAMAP-
Rule:MF_04028}.
SEQUENCE 340 AA; 37981 MW; 64B5E26548A77BF8 CRC64;
MDSAAPALSP ALTAHTGQSA PADLAIQIPK CPDPERYFYT SQCPDINHLR SLSILNRWLE
TELVFVGDEE DVSKLSEGEL SFYRFLFAFL SAADDLVTEN LGGLSGLFEQ KDILHYYVEQ
ECIEVVHSRV YNIIQLVLFH NNDQARREYV AGTINHPAIR AKVDWLEARV RECASVPEKF
ILMILIEGIF FAASFAAIAY LRTNNLLRVT CQSNDLISRD EAVHTTASCY IYNNYLGGHA
KPPPDRVYGL FRQAVEIEIG FIRSQAPTDS HILSPAALAA IENYVRFSAD RLLGLIHMKP
LFSAPPPDAS FPLSLMSTDK HTNFFECRST SYAGAVVNDL


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