TUT1_TRYBB
ID TUT1_TRYBB Reviewed; 976 AA.
AC Q8WQX5;
DT 12-AUG-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 66.
DE RecName: Full=Terminal uridylyltransferase 1 {ECO:0000305};
DE Short=TUTase 1 {ECO:0000303|PubMed:11893335};
DE EC=2.7.7.52 {ECO:0000269|PubMed:11893335, ECO:0000269|PubMed:15304317, ECO:0000269|PubMed:19465686, ECO:0000269|PubMed:26833087, ECO:0000269|PubMed:27744351, ECO:0000305|PubMed:20086102};
DE AltName: Full=3' terminal uridylyl transferase {ECO:0000303|PubMed:11893335};
DE Short=3' TUTase {ECO:0000303|PubMed:11893335};
DE AltName: Full=RNA editing 3' terminal uridylyltransferase 1 {ECO:0000305};
DE Short=RET1 {ECO:0000305};
DE Short=RNA editing TUTase 1 {ECO:0000305};
DE Flags: Precursor;
GN Name=KRET1 {ECO:0000305};
OS Trypanosoma brucei brucei.
OC Eukaryota; Discoba; Euglenozoa; Kinetoplastea; Metakinetoplastina;
OC Trypanosomatida; Trypanosomatidae; Trypanosoma.
OX NCBI_TaxID=5702;
RN [1] {ECO:0000312|EMBL:AAK38334.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=11893335; DOI=10.1016/s0092-8674(02)00647-5;
RA Aphasizhev R., Sbicego S., Peris M., Jang S.H., Aphasizheva I.,
RA Simpson A.M., Rivlin A., Simpson L.;
RT "Trypanosome mitochondrial 3' terminal uridylyl transferase (TUTase): the
RT key enzyme in U-insertion/deletion RNA editing.";
RL Cell 108:637-648(2002).
RN [2] {ECO:0000305}
RP CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=15304317; DOI=10.1016/j.febslet.2004.07.004;
RA Aphasizhev R., Aphasizheva I., Simpson L.;
RT "Multiple terminal uridylyltransferases of trypanosomes.";
RL FEBS Lett. 572:15-18(2004).
RN [3] {ECO:0000305}
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBCELLULAR
RP LOCATION.
RX PubMed=19465686; DOI=10.1261/rna.1538809;
RA Aphasizheva I., Ringpis G.E., Weng J., Gershon P.D., Lathrop R.H.,
RA Aphasizhev R.;
RT "Novel TUTase associates with an editosome-like complex in mitochondria of
RT Trypanosoma brucei.";
RL RNA 15:1322-1337(2009).
RN [4] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RX PubMed=20086102; DOI=10.1128/mcb.01281-09;
RA Aphasizheva I., Aphasizhev R.;
RT "RET1-catalyzed uridylylation shapes the mitochondrial transcriptome in
RT Trypanosoma brucei.";
RL Mol. Cell. Biol. 30:1555-1567(2010).
RN [5] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION IN THE MPSOME COMPLEX,
RP INTERACTION WITH DSS1, MPSS1 AND MPSS3, SUBCELLULAR LOCATION, DEVELOPMENTAL
RP STAGE, IDENTIFICATION BY MASS SPECTROMETRY, AND DISRUPTION PHENOTYPE.
RX PubMed=26833087; DOI=10.1016/j.molcel.2016.01.004;
RA Suematsu T., Zhang L., Aphasizheva I., Monti S., Huang L., Wang Q.,
RA Costello C.E., Aphasizhev R.;
RT "Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial
RT 3' Processome to Generate Guide RNAs.";
RL Mol. Cell 61:364-378(2016).
RN [6] {ECO:0007744|PDB:5HZD, ECO:0007744|PDB:5I49, ECO:0007744|PDB:5IDO}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 189-699 AND MUTANT ALA-473 IN
RP COMPLEX WITH ZINC; MAGNESIUM AND UTP, FUNCTION, CATALYTIC ACTIVITY,
RP COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, IDENTIFICATION IN THE
RP MPSOME COMPLEX, SUBCELLULAR LOCATION, DOMAIN, MOTIF, DEVELOPMENTAL STAGE,
RP AND DISRUPTION PHENOTYPE.
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 is involved in the post-
CC transcriptional editing of mitochondrial RNA, a process involving the
CC addition and deletion of uridine (U) nucleotides in the pre-RNA
CC (PubMed:11893335, PubMed:20086102, PubMed:26833087, PubMed:27744351).
CC Specifically, catalyzes the addition of Us to the 3'-hydroxyl group of
CC guided RNA (gRNA), ribosomal RNA (rRNA) and some mRNAs
CC (PubMed:11893335, PubMed:20086102, PubMed:26833087, PubMed:27744351).
CC As part of the mitochondrial 3' processome (MPsome), catalyzes the
CC primary 3' uridylation of gRNA precursors to facilitate their
CC recognition and to induce their processive 3'-5' degradation by DSS1,
CC and the secondary 3' uridylation of mature gRNAs (PubMed:26833087).
CC Involved in the 3' uridylylation of the long A/U tail of some edited
CC and never-edited mRNAs (PubMed:20086102). Promotes 3' uridylylation-
CC mediated decay of some never-edited mRNAs (PubMed:20086102). Does not
CC mediate RNA-independent UTP polymerization (PubMed:27744351).
CC {ECO:0000269|PubMed:11893335, ECO:0000269|PubMed:20086102,
CC ECO:0000269|PubMed:26833087, ECO:0000269|PubMed:27744351}.
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:11893335, ECO:0000269|PubMed:15304317,
CC ECO:0000269|PubMed:19465686, ECO:0000269|PubMed:26833087,
CC ECO:0000269|PubMed:27744351, ECO:0000305|PubMed:20086102};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15304317, ECO:0000305|PubMed:27744351};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q8WQX6};
CC Note=Binds 1 Mg(2+) or Mn(2+) per subunit (PubMed:27744351). The type
CC of divalent cation used by the enzyme affects the nucleotide
CC specificity; Mg(2+) induces predominantly uridine (U) incorporation
CC while Mn(2+) induces also substantial incorporation of both adenine (A)
CC and cytosine (C) (By similarity). {ECO:0000250|UniProtKB:Q8WQX6,
CC ECO:0000269|PubMed:27744351};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=17 uM for UTP (with 6(U) single-stranded RNA as substrate)
CC {ECO:0000269|PubMed:19465686};
CC KM=1.5 uM for UTP (with double-stranded RNA as substrate)
CC {ECO:0000269|PubMed:19465686};
CC KM=8.5 uM for UTP (at 27 degrees Celsius)
CC {ECO:0000269|PubMed:27744351};
CC KM=0.53 uM for RNA (at 27 degrees Celsius)
CC {ECO:0000269|PubMed:27744351};
CC Note=KM is 18-28 mM for UTP (at 27 degrees Celsius and 12 (U) single-
CC stranded RNA as substrate) (PubMed:15304317). kcat is 100 min(-1)
CC with UTP and 6(U) single-stranded RNA as substrates
CC (PubMed:19465686). kcat is 0.0012 min(-1) with UTP and double-
CC stranded RNA as substrates (PubMed:19465686). kcat is 15.5 min(-1)
CC with UTP as substrate (PubMed:27744351). kcat is 23.5 min(-1) with
CC RNA as substrate (PubMed:27744351). {ECO:0000269|PubMed:15304317,
CC ECO:0000269|PubMed:19465686, ECO:0000269|PubMed:27744351};
CC -!- SUBUNIT: Oligomer (PubMed:27744351). Component of the mitochondrial 3'
CC processome (MPsome) complex composed at least of terminal
CC uridylyltransferase KRET1/TUT1, 3'-5' exonuclease DSS1, MPSS1, MPSS2
CC and MPSS3 (PubMed:26833087, PubMed:27744351). Within the complex,
CC interacts with DSS1, MPSS1 and MPSS3 (PubMed:26833087).
CC {ECO:0000269|PubMed:26833087, ECO:0000269|PubMed:27744351}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:19465686,
CC ECO:0000269|PubMed:26833087, ECO:0000269|PubMed:27744351}.
CC -!- DEVELOPMENTAL STAGE: Expressed at the procyclic stage (at protein
CC level). {ECO:0000269|PubMed:26833087, ECO:0000269|PubMed:27744351}.
CC -!- DOMAIN: The C2H2-type zinc finger domain is required for the proper
CC folding of the catalytic domain, but is dispensable for uridylation of
CC single strand RNA substrate. {ECO:0000269|PubMed:27744351}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown at the procyclic stage
CC causes severe growth defect and a severe reduction in mRNA editing
CC (PubMed:11893335, PubMed:20086102, PubMed:26833087, PubMed:27744351).
CC Reduced production of guided RNAs (gRNA) and rRNAs due to a block in
CC the processing of gRNA and rRNA precursors (PubMed:20086102,
CC PubMed:26833087). Accumulation of unprocessed precursors for some pre-
CC edited and never-edited mRNAs (PubMed:20086102).
CC {ECO:0000269|PubMed:11893335, ECO:0000269|PubMed:20086102,
CC ECO:0000269|PubMed:26833087, ECO:0000269|PubMed:27744351}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B-like family.
CC {ECO:0000305}.
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DR EMBL; AY029070; AAK38334.1; -; Genomic_DNA.
DR PDB; 5HZD; X-ray; 1.60 A; A=189-699.
DR PDB; 5I49; X-ray; 1.80 A; A=189-699.
DR PDB; 5IDO; X-ray; 2.20 A; A=189-699.
DR PDBsum; 5HZD; -.
DR PDBsum; 5I49; -.
DR PDBsum; 5IDO; -.
DR AlphaFoldDB; Q8WQX5; -.
DR SMR; Q8WQX5; -.
DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
DR GO; GO:0032991; C:protein-containing complex; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0050265; F:RNA uridylyltransferase activity; IDA:UniProtKB.
DR GO; GO:0080156; P:mitochondrial mRNA modification; IMP:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0051260; P:protein homooligomerization; IDA:UniProtKB.
DR GO; GO:0071076; P:RNA 3' uridylation; IDA:UniProtKB.
DR GO; GO:0000154; P:rRNA modification; IMP:UniProtKB.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR002058; PAP_assoc.
DR Pfam; PF03828; PAP_assoc; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Magnesium; Manganese; Metal-binding; Mitochondrion;
KW mRNA processing; Nucleotide-binding; Nucleotidyltransferase; RNA-binding;
KW Transferase; Transit peptide; Zinc; Zinc-finger.
FT TRANSIT 1..?
FT /note="Mitochondrion"
FT /evidence="ECO:0000305"
FT CHAIN ?..976
FT /note="Terminal uridylyltransferase 1"
FT /id="PRO_0000450678"
FT DOMAIN 366..425
FT /note="PAP-associated"
FT /evidence="ECO:0000255"
FT ZN_FING 190..221
FT /note="C2H2-type; atypical"
FT /evidence="ECO:0000269|PubMed:27744351"
FT REGION 1..188
FT /note="Required for oligomerization and may contribute to
FT the incorporation into the MPsome complex"
FT /evidence="ECO:0000269|PubMed:27744351"
FT REGION 1..47
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 129..185
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 700..976
FT /note="Important for catalytic activity and RNA binding"
FT /evidence="ECO:0000269|PubMed:27744351"
FT REGION 732..755
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 652..661
FT /note="Nucleotide recognition motif (NRM)"
FT /evidence="ECO:0000305|PubMed:27744351"
FT COMPBIAS 9..47
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 151..179
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 732..752
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 195
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:5HZD, ECO:0007744|PDB:5I49"
FT BINDING 198
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:5HZD, ECO:0007744|PDB:5I49"
FT BINDING 212
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:5HZD, ECO:0007744|PDB:5I49"
FT BINDING 217
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:5HZD, ECO:0007744|PDB:5I49"
FT BINDING 298
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000250|UniProtKB:Q381M1"
FT BINDING 309..312
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000250|UniProtKB:Q381M1"
FT BINDING 310
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q86MV5"
FT BINDING 312
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q86MV5"
FT BINDING 358
FT /ligand="RNA"
FT /ligand_id="ChEBI:CHEBI:33697"
FT /evidence="ECO:0000250|UniProtKB:Q381M1"
FT BINDING 480..484
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:5I49, ECO:0007744|PDB:5IDO"
FT BINDING 505
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:5I49, ECO:0007744|PDB:5IDO"
FT BINDING 509
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:5I49, ECO:0007744|PDB:5IDO"
FT BINDING 523..524
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:27744351,
FT ECO:0007744|PDB:5I49, ECO:0007744|PDB:5IDO"
FT SITE 473
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000250|UniProtKB:Q86MV5"
FT STRAND 196..200
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 202..205
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 206..217
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 224..234
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 238..244
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 246..263
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 267..287
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 292..297
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 298..301
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 307..309
FT /evidence="ECO:0007829|PDB:5I49"
FT STRAND 311..316
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 318..322
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 330..343
FT /evidence="ECO:0007829|PDB:5HZD"
FT TURN 348..350
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 351..354
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 361..364
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 382..384
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 385..392
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 396..410
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 414..420
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 424..433
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 434..441
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 454..463
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 466..469
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 472..475
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 479..491
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 497..510
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 516..518
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 523..536
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 545..547
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 572..595
FT /evidence="ECO:0007829|PDB:5HZD"
FT TURN 599..601
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 602..604
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 606..610
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 615..617
FT /evidence="ECO:0007829|PDB:5HZD"
FT STRAND 655..657
FT /evidence="ECO:0007829|PDB:5HZD"
FT TURN 662..665
FT /evidence="ECO:0007829|PDB:5HZD"
FT HELIX 668..684
FT /evidence="ECO:0007829|PDB:5HZD"
SQ SEQUENCE 976 AA; 107524 MW; 5B497C08732D393E CRC64;
MVSKYHRLLQ QGLREEEEGV TERNMVAGGE QRHGHVDDDN AEGDADFYDQ KDERRAKMWN
PKHESANVSA GGKQNRSVRD CLPGSLPPVA NTSTDAAVRF DRERKNAGHG VDISCVEGDG
AQMGTYVSTG RSDAKAGGGS SAIGVTADDE SDGNLDTDGS DASEGDEVES TTDADVYGED
DTTEGPRGGV RLYSCDACPH AVFTTHAALL AHAEEHHADL LPDHARLRRI AQKLNPVWNR
ALNARRNTIT SWGKKIFHVA AQRDAGESKM QEAHRARAQL ECVVRRWHDK ARVFIFGSSV
AMGVWDGTAD IDFAVVDVDA MERGSWPPLE KNAVRSITEL LRRVGFSFVN LEPISHARVP
IIKHHASSPI LTVARRDAED VVARSIRFIL NGPATREDRL LLEGSVRDAV GPTGVQQVWW
NRTSDMMSAT LESTTAAVRA AMCSPALASA SLRTKVQPAH DECRPELYNI DFDLSFRAFG
IRNSTLLRKY LLSHPCARPG AIVLKDWSKT SGVNNSVNGY FTSYAINIMW IYYLVQKGYV
PYVDPLEIPE SLVNYTDFDP RYTPMIDPEI TNTEREELYK AAGDMLVGFF YFYSFEFDWG
HNVISLNRPG ITTKRMLGWH VEDVVPVAST SVSSGGGGSN VKRHPTRYEL CIEDPYEENL
NLGRHIGVTK SLRVRTELYR GLLSLLKEGE TRSCVFAAAD SSGTPAAGGK QSAALPARAL
FKLMALTTQA ISESRRLPQS NSDNSGRIAN GDNESLTEVG GGHRVEGAGV DPASCAGASL
SSFGEPPIGV HEKTLESIFV EKAPMEFQLV RKVWNWHQLI HRLGYKIHRG HVMPRREVGV
RCTARRDAEE TTTELASGVD TTKSLRPGRG LTDTMLRDLS RGYMTLTPEW VAWSAPWVSQ
HLRGYSRLTT VRSAVADETP PALATVPSVV KPPTGEAVMG AMRTTRRNAA PARRVELLKL
WLWRGISKVT PFKSPR
