TRNL_CANAL
ID TRNL_CANAL Reviewed; 832 AA.
AC P43075; A0A1D8PR09; Q3MPD7; Q5AH27;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 19-OCT-2011, sequence version 2.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=tRNA ligase;
DE EC=6.5.1.3 {ECO:0000305};
GN Name=LIG1; Synonyms=RLG1, TRL1; OrderedLocusNames=CAALFM_C702060WA;
GN ORFNames=CaJ7.0238, CaO19.13864, CaO19.6511;
OS Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Debaryomycetaceae; Candida/Lodderomyces clade; Candida.
OX NCBI_TaxID=237561;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=8181747; DOI=10.1016/0378-1119(94)90367-0;
RA Baymiller J., Jennings S., Kienzle B., Gorman J.A., Kelly R.,
RA McCullough J.E.;
RT "Isolation and sequence of the t-RNA ligase-encoding gene of Candida
RT albicans.";
RL Gene 142:129-134(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=15937140; DOI=10.1534/genetics.104.034652;
RA Chibana H., Oka N., Nakayama H., Aoyama T., Magee B.B., Magee P.T.,
RA Mikami Y.;
RT "Sequence finishing and gene mapping for Candida albicans chromosome 7 and
RT syntenic analysis against the Saccharomyces cerevisiae genome.";
RL Genetics 170:1525-1537(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=15123810; DOI=10.1073/pnas.0401648101;
RA Jones T., Federspiel N.A., Chibana H., Dungan J., Kalman S., Magee B.B.,
RA Newport G., Thorstenson Y.R., Agabian N., Magee P.T., Davis R.W.,
RA Scherer S.;
RT "The diploid genome sequence of Candida albicans.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:7329-7334(2004).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=17419877; DOI=10.1186/gb-2007-8-4-r52;
RA van het Hoog M., Rast T.J., Martchenko M., Grindle S., Dignard D.,
RA Hogues H., Cuomo C., Berriman M., Scherer S., Magee B.B., Whiteway M.,
RA Chibana H., Nantel A., Magee P.T.;
RT "Assembly of the Candida albicans genome into sixteen supercontigs aligned
RT on the eight chromosomes.";
RL Genome Biol. 8:RESEARCH52.1-RESEARCH52.12(2007).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND GENOME REANNOTATION.
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=24025428; DOI=10.1186/gb-2013-14-9-r97;
RA Muzzey D., Schwartz K., Weissman J.S., Sherlock G.;
RT "Assembly of a phased diploid Candida albicans genome facilitates allele-
RT specific measurements and provides a simple model for repeat and indel
RT structure.";
RL Genome Biol. 14:RESEARCH97.1-RESEARCH97.14(2013).
CC -!- FUNCTION: One of the two proteins required for the splicing of
CC precursor tRNA molecules containing introns. The ligation activity
CC requires three enzymatic activities: phosphorylation of the 5' terminus
CC of the 3' half-tRNA in the presence of ATP, opening of the 2'3'-cyclic
CC phosphodiester bond of the 5' half-tRNA leaving a 2'-phosphomonoester
CC and ligation of the two tRNA halves in an ATP-dependent reaction.
CC {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate.;
CC EC=6.5.1.3; Evidence={ECO:0000305};
CC -!- DOMAIN: Has three domains each corresponding to an enzymatic activity,
CC namely in N- to C-terminal order: ligase, kinase and cyclic
CC phosphodiesterase (CPDase). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the TRL1 family. {ECO:0000305}.
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DR EMBL; L13380; AAA34373.2; -; Genomic_DNA.
DR EMBL; AP006852; BAE44723.1; -; Genomic_DNA.
DR EMBL; CP017629; AOW30569.1; -; Genomic_DNA.
DR RefSeq; XP_721349.1; XM_716256.2.
DR PDB; 5U32; X-ray; 2.19 A; A=400-635.
DR PDB; 6TZM; X-ray; 1.71 A; A=401-832.
DR PDB; 6TZO; X-ray; 1.69 A; A=401-832.
DR PDB; 6TZX; X-ray; 1.53 A; A=401-635.
DR PDB; 6U00; X-ray; 1.98 A; A/B=401-832.
DR PDB; 6U03; X-ray; 1.85 A; A=401-635.
DR PDB; 6U05; X-ray; 1.95 A; A=401-832.
DR PDBsum; 5U32; -.
DR PDBsum; 6TZM; -.
DR PDBsum; 6TZO; -.
DR PDBsum; 6TZX; -.
DR PDBsum; 6U00; -.
DR PDBsum; 6U03; -.
DR PDBsum; 6U05; -.
DR AlphaFoldDB; P43075; -.
DR SMR; P43075; -.
DR STRING; 237561.P43075; -.
DR PRIDE; P43075; -.
DR GeneID; 3636947; -.
DR KEGG; cal:CAALFM_C702060WA; -.
DR CGD; CAL0000175809; LIG1.
DR VEuPathDB; FungiDB:C7_02060W_A; -.
DR eggNOG; ENOG502QQB9; Eukaryota.
DR HOGENOM; CLU_010316_1_0_1; -.
DR InParanoid; P43075; -.
DR OrthoDB; 343868at2759; -.
DR Proteomes; UP000000559; Chromosome 7.
DR GO; GO:0005637; C:nuclear inner membrane; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0051730; F:GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity; IDA:CGD.
DR GO; GO:0008081; F:phosphoric diester hydrolase activity; IEA:InterPro.
DR GO; GO:0003972; F:RNA ligase (ATP) activity; IDA:CGD.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IGI:CGD.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR019039; RNA_ligase_T4-Rnl1_N.
DR InterPro; IPR012387; Trl1_fun.
DR InterPro; IPR015966; tRNA_lig_kin_fungi.
DR InterPro; IPR015965; tRNA_lig_PDEase.
DR Pfam; PF09511; RNA_lig_T4_1; 1.
DR Pfam; PF08302; tRNA_lig_CPD; 1.
DR Pfam; PF08303; tRNA_lig_kinase; 1.
DR PIRSF; PIRSF019634; tRNA_lig_yeast; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Endonuclease; Hydrolase; Kinase; Ligase;
KW Multifunctional enzyme; Nuclease; Nucleotide-binding; Reference proteome;
KW Transferase; tRNA processing.
FT CHAIN 1..832
FT /note="tRNA ligase"
FT /id="PRO_0000065634"
FT ACT_SITE 108
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000250"
FT CONFLICT 542
FT /note="Q -> K (in Ref. 1; AAA34373)"
FT /evidence="ECO:0000305"
FT CONFLICT 783
FT /note="I -> M (in Ref. 1; AAA34373)"
FT /evidence="ECO:0000305"
FT STRAND 410..418
FT /evidence="ECO:0007829|PDB:6TZX"
FT HELIX 425..435
FT /evidence="ECO:0007829|PDB:6TZX"
FT STRAND 439..443
FT /evidence="ECO:0007829|PDB:6TZX"
FT HELIX 444..446
FT /evidence="ECO:0007829|PDB:6TZX"
FT HELIX 455..464
FT /evidence="ECO:0007829|PDB:6TZX"
FT STRAND 470..475
FT /evidence="ECO:0007829|PDB:6TZX"
FT HELIX 480..493
FT /evidence="ECO:0007829|PDB:6TZX"
FT HELIX 494..496
FT /evidence="ECO:0007829|PDB:6TZX"
FT STRAND 502..510
FT /evidence="ECO:0007829|PDB:6TZX"
FT HELIX 518..532
FT /evidence="ECO:0007829|PDB:6TZX"
FT HELIX 537..539
FT /evidence="ECO:0007829|PDB:6TZX"
FT HELIX 545..558
FT /evidence="ECO:0007829|PDB:6TZX"
FT HELIX 569..571
FT /evidence="ECO:0007829|PDB:6TZX"
FT STRAND 573..577
FT /evidence="ECO:0007829|PDB:6TZX"
FT STRAND 582..584
FT /evidence="ECO:0007829|PDB:6U00"
FT HELIX 589..604
FT /evidence="ECO:0007829|PDB:6TZX"
FT TURN 606..608
FT /evidence="ECO:0007829|PDB:6TZX"
FT STRAND 609..611
FT /evidence="ECO:0007829|PDB:6TZM"
FT HELIX 615..627
FT /evidence="ECO:0007829|PDB:6TZX"
FT TURN 634..636
FT /evidence="ECO:0007829|PDB:6U05"
FT STRAND 646..652
FT /evidence="ECO:0007829|PDB:6U05"
FT HELIX 654..659
FT /evidence="ECO:0007829|PDB:6U05"
FT TURN 660..666
FT /evidence="ECO:0007829|PDB:6U05"
FT HELIX 668..670
FT /evidence="ECO:0007829|PDB:6U05"
FT HELIX 671..674
FT /evidence="ECO:0007829|PDB:6U05"
FT STRAND 679..687
FT /evidence="ECO:0007829|PDB:6U05"
FT HELIX 688..692
FT /evidence="ECO:0007829|PDB:6U05"
FT HELIX 695..707
FT /evidence="ECO:0007829|PDB:6U05"
FT STRAND 713..734
FT /evidence="ECO:0007829|PDB:6U05"
FT TURN 735..737
FT /evidence="ECO:0007829|PDB:6U05"
FT STRAND 738..750
FT /evidence="ECO:0007829|PDB:6U05"
FT STRAND 767..772
FT /evidence="ECO:0007829|PDB:6U05"
FT HELIX 780..788
FT /evidence="ECO:0007829|PDB:6U05"
FT STRAND 800..805
FT /evidence="ECO:0007829|PDB:6U05"
FT STRAND 808..814
FT /evidence="ECO:0007829|PDB:6U05"
FT STRAND 821..830
FT /evidence="ECO:0007829|PDB:6U05"
SQ SEQUENCE 832 AA; 95551 MW; 08617FF2127868B3 CRC64;
MKDSQSDIIE LCNKLNEATK LKRNGKSIKL TNFVSNTQIK LDSWKFLEWD YGKPSVQLPI
QARGLFTLNN DTIAVRGYDK FFNVEEKPFT KETNLKTSTH GPYEVTLKEN GCIIFISGLS
TGDIVVCSKH STGDRIDDNE SDKTTTATAT ATAPTRNHAK QGEFELLQQF DGDQQKVKQL
AHYLYENNLT VVAELCDDEF EEHVLPYPKD KSGLYVHGLN YNTITFKTLP MDQVLQFAKE
WGFKYVSYLT YDNADELFKF LHKCSETGTY NGREIEGFVI RCHRQSHTNG DTDGDCFFFK
YKFEQPYLLY RQFREVTKQL LNGTPINSIK IKKNKPITKK YLQFVEKLFE QEPEIARNFE
NGFDIIKVRQ LFLQSLNETN GMNLLSIDSE LSDQLKNLAL ANGNEGLSTT TKYIFVPIAT
IGCGKTTVFN TLNNLFPQWT HIQNDNISKK AKLKICDLTL LALEDDDQSV VLFDRNNSAS
RERRQIFTTI DQKRDEHLDD TVDLKYIAIN FIPEDLSEEE LWDITYNRVI QRGDNHQSIK
SQSDENLVES VMKGFIQRYQ PINTSRSPDD QFDHVIHLKL SKDENSSKSS LENVRIIIDD
LVQNFPDLIK EKPADELINE CFQKALDYKP TFVKNMTANT IKKDPTYYGI AMHYSSILEN
LEIVSHNEHF QNIKSHIQTE FHVTLGHIAS SKQDKAGRVK WKKLVKTLGK GDPNKPKSAL
KFFADVKLLQ IVINTDKLAC IKVEILKIYD TNDVLQSEIE PINKQLHITI GCIPPATAVE
SNITLEELYD NPDEQELKPD GTYKCGDDTL HVFNFDNPDL KLFSQQLFVA YQ
