TUT4_TRYB2
ID TUT4_TRYB2 Reviewed; 333 AA.
AC Q381M1; A4UBD5;
DT 12-AUG-2020, integrated into UniProtKB/Swiss-Prot.
DT 22-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=Terminal uridylyltransferase 4 {ECO:0000303|PubMed:17189640};
DE Short=TUTase 4 {ECO:0000305};
DE EC=2.7.7.52 {ECO:0000269|PubMed:17189640, ECO:0000269|PubMed:17785418};
DE AltName: Full=3' terminal uridylyl transferase {ECO:0000305};
DE AltName: Full=RNA editing 3' terminal uridylyltransferase 4 {ECO:0000305};
DE AltName: Full=RNA uridylyltransferase 4 {ECO:0000303|PubMed:17189640};
GN Name=TUT4 {ECO:0000303|PubMed:17189640};
GN ORFNames=Tb11.01.7300 {ECO:0000312|EMBL:EAN80510.1};
OS Trypanosoma brucei brucei (strain 927/4 GUTat10.1).
OC Eukaryota; Discoba; Euglenozoa; Kinetoplastea; Metakinetoplastina;
OC Trypanosomatida; Trypanosomatidae; Trypanosoma.
OX NCBI_TaxID=185431 {ECO:0000312|Proteomes:UP000008524};
RN [1] {ECO:0007744|PDB:2IKF, ECO:0007744|PDB:2NOM}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS)
RP IN COMPLEX WITH UTP AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MUTAGENESIS OF PHE-52; ASP-66;
RP ASP-68; ARG-121; ARG-126; ASP-136; ARG-141; ASN-147; SER-148; SER-188;
RP TYR-189; ASP-297; GLU-300 AND ARG-307.
RX PubMed=17189640; DOI=10.1016/j.jmb.2006.11.065;
RA Stagno J., Aphasizheva I., Rosengarth A., Luecke H., Aphasizhev R.;
RT "UTP-bound and Apo structures of a minimal RNA uridylyltransferase.";
RL J. Mol. Biol. 366:882-899(2007).
RN [2] {ECO:0000312|Proteomes:UP000008524}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=927/4 GUTat10.1 {ECO:0000312|Proteomes:UP000008524};
RX PubMed=16020726; DOI=10.1126/science.1112642;
RA Berriman M., Ghedin E., Hertz-Fowler C., Blandin G., Renauld H.,
RA Bartholomeu D.C., Lennard N.J., Caler E., Hamlin N.E., Haas B., Bohme U.,
RA Hannick L., Aslett M.A., Shallom J., Marcello L., Hou L., Wickstead B.,
RA Alsmark U.C.M., Arrowsmith C., Atkin R.J., Barron A.J., Bringaud F.,
RA Brooks K., Carrington M., Cherevach I., Chillingworth T.J., Churcher C.,
RA Clark L.N., Corton C.H., Cronin A., Davies R.M., Doggett J., Djikeng A.,
RA Feldblyum T., Field M.C., Fraser A., Goodhead I., Hance Z., Harper D.,
RA Harris B.R., Hauser H., Hostetler J., Ivens A., Jagels K., Johnson D.,
RA Johnson J., Jones K., Kerhornou A.X., Koo H., Larke N., Landfear S.,
RA Larkin C., Leech V., Line A., Lord A., Macleod A., Mooney P.J., Moule S.,
RA Martin D.M., Morgan G.W., Mungall K., Norbertczak H., Ormond D., Pai G.,
RA Peacock C.S., Peterson J., Quail M.A., Rabbinowitsch E., Rajandream M.A.,
RA Reitter C., Salzberg S.L., Sanders M., Schobel S., Sharp S., Simmonds M.,
RA Simpson A.J., Tallon L., Turner C.M., Tait A., Tivey A.R., Van Aken S.,
RA Walker D., Wanless D., Wang S., White B., White O., Whitehead S.,
RA Woodward J., Wortman J., Adams M.D., Embley T.M., Gull K., Ullu E.,
RA Barry J.D., Fairlamb A.H., Opperdoes F., Barrell B.G., Donelson J.E.,
RA Hall N., Fraser C.M., Melville S.E., El-Sayed N.M.A.;
RT "The genome of the African trypanosome Trypanosoma brucei.";
RL Science 309:416-422(2005).
RN [3] {ECO:0007744|PDB:2Q0C, ECO:0007744|PDB:2Q0D, ECO:0007744|PDB:2Q0E}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH UTP; RNA ANALOG AND
RP MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, AND ACTIVITY REGULATION.
RX PubMed=17785418; DOI=10.1073/pnas.0704259104;
RA Stagno J., Aphasizheva I., Aphasizhev R., Luecke H.;
RT "Dual role of the RNA substrate in selectivity and catalysis by terminal
RT uridylyl transferases.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:14634-14639(2007).
RN [4] {ECO:0007744|PDB:5KAL}
RP X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) IN COMPLEX WITH UTP; RNA ANALOG AND
RP MAGNESIUM.
RX PubMed=27744351; DOI=10.1093/nar/gkw917;
RA Rajappa-Titu L., Suematsu T., Munoz-Tello P., Long M., Demir O.,
RA Cheng K.J., Stagno J.R., Luecke H., Amaro R.E., Aphasizheva I.,
RA Aphasizhev R., Thore S.;
RT "RNA Editing TUTase 1: structural foundation of substrate recognition,
RT complex interactions and drug targeting.";
RL Nucleic Acids Res. 44:10862-10878(2016).
CC -!- FUNCTION: Terminal uridylyltransferase which, specifically, catalyzes
CC the addition of Us to the 3'-hydroxyl group of single-stranded RNAs
CC with a 3'-terminal U. {ECO:0000269|PubMed:17189640,
CC ECO:0000269|PubMed:17785418}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=RNA(n) + UTP = diphosphate + RNA(n)-3'-uridine ribonucleotide;
CC Xref=Rhea:RHEA:14785, Rhea:RHEA-COMP:14527, Rhea:RHEA-COMP:17348,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:46398, ChEBI:CHEBI:140395,
CC ChEBI:CHEBI:173116; EC=2.7.7.52;
CC Evidence={ECO:0000269|PubMed:17189640, ECO:0000269|PubMed:17785418};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:17189640, ECO:0000269|PubMed:17785418};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:17189640};
CC Note=Binds 1 Mg(2+) or Mn(2+) per subunit (PubMed:17189640,
CC PubMed:17785418). The type of divalent cation used by the enzyme
CC affects the nucleotide specificity; Mg(2+) induces predominantly
CC uridine (U) incorporation while Mn(2+) induces also substantial
CC incorporation of both adenine (A) and cytosine (C) (PubMed:17189640).
CC {ECO:0000269|PubMed:17189640, ECO:0000269|PubMed:17785418};
CC -!- ACTIVITY REGULATION: The 3' uridylated RNA substrate is involved in the
CC selective incorporation of UTP; UTP binding is favored due to the
CC constraint posed on the positioning of the NTP base by the continuous
CC stacking interactions between Tyr-189 side chain, the bound NTP, and
CC the terminal nucleoside base of the RNA substrate.
CC {ECO:0000269|PubMed:17785418}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1 uM for UTP (at 27 degrees Celsius and with 6(U) single-stranded
CC RNA as substrate);
CC KM=0.2 uM for 6(U) single-stranded RNA (at 27 degrees Celsius);
CC Note=kcat is 0.5 min(-1) with UTP (PubMed:17189640). kcat is 0.3
CC min(-1) with 6(U) single-stranded RNA (PubMed:17189640).
CC {ECO:0000269|PubMed:17189640};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:17189640}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B-like family.
CC {ECO:0000305}.
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DR EMBL; DQ923393; ABL07000.1; -; Genomic_DNA.
DR EMBL; CH464491; EAN80510.1; -; Genomic_DNA.
DR RefSeq; XP_829622.1; XM_824529.1.
DR PDB; 2IKF; X-ray; 2.00 A; A/B=1-333.
DR PDB; 2NOM; X-ray; 2.40 A; A/B=1-333.
DR PDB; 2Q0C; X-ray; 2.20 A; A/B=1-333.
DR PDB; 2Q0D; X-ray; 2.00 A; A/B=1-333.
DR PDB; 2Q0E; X-ray; 2.10 A; A/B=1-333.
DR PDB; 2Q0F; X-ray; 2.40 A; A/B=1-333.
DR PDB; 2Q0G; X-ray; 2.30 A; A/B=1-333.
DR PDB; 5KAL; X-ray; 2.75 A; A/B=1-333.
DR PDBsum; 2IKF; -.
DR PDBsum; 2NOM; -.
DR PDBsum; 2Q0C; -.
DR PDBsum; 2Q0D; -.
DR PDBsum; 2Q0E; -.
DR PDBsum; 2Q0F; -.
DR PDBsum; 2Q0G; -.
DR PDBsum; 5KAL; -.
DR AlphaFoldDB; Q381M1; -.
DR SMR; Q381M1; -.
DR STRING; 5691.EAN80510; -.
DR PaxDb; Q381M1; -.
DR EnsemblProtists; EAN80510; EAN80510; Tb11.01.7300.
DR GeneID; 3664455; -.
DR KEGG; tbr:Tb11.01.7300; -.
DR VEuPathDB; TriTrypDB:Tb927.11.15650; -.
DR eggNOG; KOG2277; Eukaryota.
DR HOGENOM; CLU_835482_0_0_1; -.
DR InParanoid; Q381M1; -.
DR BRENDA; 2.7.7.52; 6519.
DR EvolutionaryTrace; Q381M1; -.
DR Proteomes; UP000008524; Chromosome 11 Scaffold 1.
DR GO; GO:0020023; C:kinetoplast; IDA:GeneDB.
DR GO; GO:0005739; C:mitochondrion; IDA:GeneDB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0016779; F:nucleotidyltransferase activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0050265; F:RNA uridylyltransferase activity; IDA:UniProtKB.
DR GO; GO:0071076; P:RNA 3' uridylation; IDA:UniProtKB.
DR GO; GO:0031123; P:RNA 3'-end processing; IBA:GO_Central.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR002058; PAP_assoc.
DR InterPro; IPR045100; TUTase_dom.
DR Pfam; PF03828; PAP_assoc; 1.
DR Pfam; PF19088; TUTase; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW Nucleotidyltransferase; Reference proteome; RNA-binding; Transferase.
FT CHAIN 1..333
FT /note="Terminal uridylyltransferase 4"
FT /id="PRO_0000450681"
FT DOMAIN 237..302
FT /note="PAP-associated"
FT /evidence="ECO:0000255"
FT BINDING 54
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:17189640,
FT ECO:0000269|PubMed:17785418, ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:2IKF, ECO:0007744|PDB:2Q0F,
FT ECO:0007744|PDB:5KAL"
FT BINDING 65..68
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:17189640,
FT ECO:0000269|PubMed:17785418, ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:2IKF, ECO:0007744|PDB:2Q0F,
FT ECO:0007744|PDB:5KAL"
FT BINDING 66
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:17189640,
FT ECO:0000269|PubMed:17785418, ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:2IKF, ECO:0007744|PDB:2NOM,
FT ECO:0007744|PDB:2Q0C, ECO:0007744|PDB:2Q0D,
FT ECO:0007744|PDB:2Q0E, ECO:0007744|PDB:2Q0F,
FT ECO:0007744|PDB:2Q0G, ECO:0007744|PDB:5KAL"
FT BINDING 68
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:17189640,
FT ECO:0000269|PubMed:17785418, ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:2IKF, ECO:0007744|PDB:2NOM,
FT ECO:0007744|PDB:2Q0C, ECO:0007744|PDB:2Q0D,
FT ECO:0007744|PDB:2Q0E, ECO:0007744|PDB:2Q0F,
FT ECO:0007744|PDB:2Q0G, ECO:0007744|PDB:5KAL"
FT BINDING 121
FT /ligand="RNA"
FT /ligand_id="ChEBI:CHEBI:33697"
FT /evidence="ECO:0000269|PubMed:17785418,
FT ECO:0000269|PubMed:27744351, ECO:0007744|PDB:2Q0F,
FT ECO:0007744|PDB:2Q0G, ECO:0007744|PDB:5KAL"
FT BINDING 144..148
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:17189640,
FT ECO:0000269|PubMed:17785418, ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:2IKF, ECO:0007744|PDB:2Q0F,
FT ECO:0007744|PDB:5KAL"
FT BINDING 169
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:17189640,
FT ECO:0000269|PubMed:17785418, ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:2IKF, ECO:0007744|PDB:2Q0F,
FT ECO:0007744|PDB:5KAL"
FT BINDING 173
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:17189640,
FT ECO:0000269|PubMed:17785418, ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:2IKF, ECO:0007744|PDB:2Q0F,
FT ECO:0007744|PDB:5KAL"
FT BINDING 188..189
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:17189640,
FT ECO:0000269|PubMed:17785418, ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:2IKF, ECO:0007744|PDB:2Q0F,
FT ECO:0007744|PDB:5KAL"
FT SITE 136
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 52
FT /note="F->A: Loss of catalytic activity. Moderate decrease
FT in UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 66
FT /note="D->A: Loss of catalytic activity. Does not affect
FT UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 68
FT /note="D->A: Loss of catalytic activity. Partial reduction
FT in UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 121
FT /note="R->A: 2-fold decrease in affinity for UTP. 660-fold
FT decrease in affinity for RNA."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 121
FT /note="R->F: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 126
FT /note="R->A: Loss of catalytic activity. Does not affect
FT UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 136
FT /note="D->A: Loss of catalytic activity. Does not affect
FT UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 141
FT /note="R->A: Does not affect UTP binding. 360-fold decrease
FT in affinity for RNA."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 147
FT /note="N->A: Severe decrease in UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 148
FT /note="S->A: Severe decrease in UTP binding without
FT affecting RNA binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 188
FT /note="S->A: Severe decrease in UTP binding without
FT affecting RNA binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 189
FT /note="Y->A: Loss of catalytic activity. Severe decrease in
FT UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 189
FT /note="Y->F: Loss of catalytic activity. Moderate decrease
FT in UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 297
FT /note="D->A,N: Severe decrease in UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 300
FT /note="E->A: Moderate decrease in UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT MUTAGEN 307
FT /note="R->A: 50-fold decrease in affinity for RNA. Does not
FT affect UTP binding."
FT /evidence="ECO:0000269|PubMed:17189640"
FT HELIX 5..15
FT /evidence="ECO:0007829|PDB:2IKF"
FT TURN 16..19
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 26..28
FT /evidence="ECO:0007829|PDB:2Q0E"
FT HELIX 29..43
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 48..53
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 54..58
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 67..72
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 74..78
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 88..108
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 112..117
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 119..122
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 124..128
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 134..140
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 143..157
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 161..174
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 188..201
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 210..212
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 215..217
FT /evidence="ECO:0007829|PDB:2IKF"
FT TURN 231..234
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 235..250
FT /evidence="ECO:0007829|PDB:2IKF"
FT TURN 254..256
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 257..259
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 261..265
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 269..272
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 276..279
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 283..288
FT /evidence="ECO:0007829|PDB:2Q0G"
FT STRAND 292..296
FT /evidence="ECO:0007829|PDB:2IKF"
FT STRAND 298..300
FT /evidence="ECO:0007829|PDB:2IKF"
FT TURN 305..308
FT /evidence="ECO:0007829|PDB:2IKF"
FT HELIX 311..325
FT /evidence="ECO:0007829|PDB:2IKF"
FT TURN 326..331
FT /evidence="ECO:0007829|PDB:2IKF"
SQ SEQUENCE 333 AA; 37656 MW; F89A82FA1E1DEC47 CRC64;
MPPSPAVVGR SLVNSFKQFV SKDLHTRHVD ATYRLVLDCV AAVDPLMRLY TFGSTVVYGV
HEKGSDVDFV VLNKTDVEDG KGGDAATQVA KGLQADILAK LARVIRQKHL SWNVEEVRRT
RVPVVRVKGG GAVDFDITAY RRNGVRNSAL LRAYFEQNPP CRWLSMSIKR WSKQTGLNAS
VIGGSITSYG FNLMVVYYLL QRNHLQFVPP STIDVSRVEP LPPHLPLEEP ADEGLELGTQ
VLDFLHFFLH EFDSDKQVIS LNRPGITTKE ELDWTKSAED FARMNGEKVH YQWCIEDPYE
LNLNVGRNVT PLKRDFLRRH LEKARDTALL TIV
