ID   HMUD2_BPSAV             Reviewed;         304 AA.
AC   E1XTK3;
DT   03-AUG-2022, integrated into UniProtKB/Swiss-Prot.
DT   30-NOV-2010, sequence version 1.
DT   03-AUG-2022, entry version 29.
DE   RecName: Full=5-hmdU DNA kinase 2 {ECO:0000303|PubMed:34522950};
DE   AltName: Full=5-hydroxymethyluracil DNA kinase {ECO:0000303|PubMed:34522950};
DE   AltName: Full=P-loop kinase {ECO:0000303|PubMed:34522950};
DE   AltName: Full=gp243 {ECO:0000303|PubMed:34522950};
GN   ORFNames=Vi01_196 {ECO:0000312|EMBL:CBW38062.1};
OS   Salmonella phage ViI.
OC   Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC   Caudovirales; Ackermannviridae; Cvivirinae; Kuttervirus.
OX   NCBI_TaxID=1987993;
OH   NCBI_TaxID=90370; Salmonella typhi.
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=20817773; DOI=10.1128/jb.00659-10;
RA   Pickard D., Toribio A.L., Petty N.K., van Tonder A., Yu L., Goulding D.,
RA   Barrell B., Rance R., Harris D., Wetter M., Wain J., Choudhary J.,
RA   Thomson N., Dougan G.;
RT   "A conserved acetyl esterase domain targets diverse bacteriophages to the
RT   Vi capsular receptor of Salmonella enterica serovar Typhi.";
RL   J. Bacteriol. 192:5746-5754(2010).
RN   [2]
RP   FUNCTION.
RX   PubMed=29555775; DOI=10.1073/pnas.1714812115;
RA   Lee Y.J., Dai N., Walsh S.E., Mueller S., Fraser M.E., Kauffman K.M.,
RA   Guan C., Correa I.R. Jr., Weigele P.R.;
RT   "Identification and biosynthesis of thymidine hypermodifications in the
RT   genomic DNA of widespread bacterial viruses.";
RL   Proc. Natl. Acad. Sci. U.S.A. 115:E3116-E3125(2018).
RN   [3]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=34522950; DOI=10.1093/nar/gkab781;
RA   Lee Y.J., Dai N., Mueller S.I., Guan C., Parker M.J., Fraser M.E.,
RA   Walsh S.E., Sridar J., Mulholland A., Nayak K., Sun Z., Lin Y.C.,
RA   Comb D.G., Marks K., Gonzalez R., Dowling D.P., Bandarian V., Saleh L.,
RA   Correa I.R., Weigele P.R.;
RT   "Pathways of thymidine hypermodification.";
RL   Nucleic Acids Res. 0:0-0(2021).
CC   -!- FUNCTION: Phosphorylates 5-hydroxymethyluracil (5hmdU) into 5-
CC       phosphomethyl-2'-deoxyuridine (5- PmdU) on DNA as a step in the pathway
CC       leading to thymidine hypermodifications in the viral genome
CC       (PubMed:34522950). The phosphate is added internally to the DNA polymer
CC       (PubMed:34522950). As a final result of the pathway of
CC       hypermodification, 5-aminoethoxy-2'-deoxymethyluridine (5-NeOmdU)
CC       substitutes for about 40% of the thymidines in the viral DNA
CC       (PubMed:34522950, PubMed:29555775). These modifications probably
CC       prevent degradation of viral genome by the host restriction-
CC       modification antiviral defense system (PubMed:34522950).
CC       {ECO:0000269|PubMed:29555775, ECO:0000269|PubMed:34522950}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=5-hydroxymethyl-dUMP in DNA + ATP = 5-phosphomethyl-dUMP in
CC         DNA + ADP + H(+); Xref=Rhea:RHEA:71543, Rhea:RHEA-COMP:18039,
CC         Rhea:RHEA-COMP:18041, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC         ChEBI:CHEBI:190917, ChEBI:CHEBI:190918, ChEBI:CHEBI:456216;
CC         Evidence={ECO:0000269|PubMed:34522950};
CC   -!- SIMILARITY: Belongs to the thymidylate kinase family. 5-hmdU DNA kinase
CC       subfamily. {ECO:0000305}.
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DR   EMBL; FQ312032; CBW38062.1; -; Genomic_DNA.
DR   Proteomes; UP000000339; Genome.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR041021; Ploopntkinase2.
DR   Pfam; PF18747; Ploopntkinase2; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
PE   1: Evidence at protein level;
KW   Host-virus interaction; Reference proteome;
KW   Restriction-modification system evasion by virus.
FT   CHAIN           1..304
FT                   /note="5-hmdU DNA kinase 2"
FT                   /id="PRO_0000456269"
SQ   SEQUENCE   304 AA;  34014 MW;  566B2C6082405AF9 CRC64;
     MAKIIVIKGT SGTGKGTRVV QFIEWLRTKL KPTELSYTVG DKTRPFGLKF EELKLIFVGQ
     YTVSNKSGLA SWTSMDAIHA ATGSGDIARD LVKGWLAQGY TLVCEGEPLM LSDKWRPEWM
     FKNYPIDSLA LLYFAYPDRY QYDARIRGRS GKEAGDSGWS RNESYSKEFE KSKAEMLALG
     WNVAVDDYSG QDVLYHQTAT NTQEFKTGND SELAMLPFDA PLWVVGNAIY HQLGTVCRAN
     NLMSKDFYGY CETNPMTREV GGQDPLAHRV PEKPQKASKT KNKAVAKEEP KTSSVSLLGL
     MRKA