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Protein

Pre-mRNA-splicing factor CLF1

Gene

CLF1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in pre-mRNA splicing and cell cycle progression. Required for the spliceosome assembly by promoting the functional integration of the U4/U6.U5 tri-snRNP particle into the U1-, U2-dependent pre-spliceosome. Also recruits PRP19 to the spliceosome, as a component of the NTC complex (or PRP19-associated complex). The association of the NTC complex to the spliceosome mediates conformational rearrangement or stabilizes the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. Required for initiation of the DNA replication by binding the RNA replication origins, probably through its interaction with the origin recognition complex (ORC).5 Publications

Miscellaneous

Present with 2140 molecules/cell in log phase SD medium.1 Publication

GO - Molecular functioni

  • chromatin binding Source: SGD
  • DNA replication origin binding Source: SGD

GO - Biological processi

  • cis assembly of pre-catalytic spliceosome Source: SGD
  • DNA replication initiation Source: SGD

Keywordsi

Biological processmRNA processing, mRNA splicing

Enzyme and pathway databases

BioCyciYEAST:G3O-32262-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-splicing factor CLF1
Alternative name(s):
Crooked neck-like factor 1
PRP19-associated complex protein 77
Synthetic lethal with CDC40 protein 3
Gene namesi
Name:CLF1
Synonyms:NTC77, SYF3
Ordered Locus Names:YLR117C
ORF Names:L2952
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR117C.
SGDiS000004107. CLF1.

Subcellular locationi

GO - Cellular componenti

  • chromatin Source: SGD
  • precatalytic spliceosome Source: GO_Central
  • Prp19 complex Source: SGD
  • U2-type catalytic step 1 spliceosome Source: SGD
  • U2-type catalytic step 2 spliceosome Source: SGD
  • U2-type post-mRNA release spliceosomal complex Source: SGD
  • U2-type prespliceosome Source: SGD

Keywords - Cellular componenti

Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002057531 – 687Pre-mRNA-splicing factor CLF1Add BLAST687

Proteomic databases

MaxQBiQ12309.
PRIDEiQ12309.

Interactioni

Subunit structurei

Belongs to the NTC complex (or PRP19-associated complex), composed of at least CEF1, CLF1, ISY1, NTC20, SNT309, SYF1, SYF2, and PRP19. The NTC complex associates with the spliceosome after the release of the U1 and U4 snRNAs and forms the CWC spliceosome subcomplex (or CEF1-associated complex) reminiscent of a late-stage spliceosome composed also of the U2, U5 and U6 snRNAs and at least BUD13, BUD31, BRR2, CDC40, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3, LEA1, MSL1, PRP8, PRP9, PRP11, PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, SNU114, SPP2, RSE1 and YJU2. Interacts with CEF1, ISY1, MUD2, NTC20, PRP22, PRP40, PRP46, SYF1, SYF2, and the ORC2 subunit of the origin recognition complex.8 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi31389. 279 interactors.
DIPiDIP-1685N.
IntActiQ12309. 35 interactors.
MINTiMINT-385873.
STRINGi4932.YLR117C.

Structurei

Secondary structure

1687
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi40 – 60Combined sources21
Helixi65 – 77Combined sources13
Helixi81 – 94Combined sources14
Helixi99 – 111Combined sources13
Helixi115 – 128Combined sources14
Helixi133 – 144Combined sources12
Turni145 – 147Combined sources3
Helixi149 – 161Combined sources13
Helixi166 – 178Combined sources13
Helixi182 – 195Combined sources14
Helixi199 – 212Combined sources14
Helixi215 – 232Combined sources18
Helixi233 – 235Combined sources3
Helixi240 – 256Combined sources17
Helixi260 – 273Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5GM6electron microscopy3.50d1-275[»]
5GMKelectron microscopy3.40d1-275[»]
5LJ3electron microscopy3.80S1-687[»]
5LJ5electron microscopy3.80S1-687[»]
5LQWelectron microscopy5.80R1-687[»]
5MPSelectron microscopy3.85S1-687[»]
5MQ0electron microscopy4.17S1-687[»]
5WSGelectron microscopy4.00d36-275[»]
ProteinModelPortaliQ12309.
SMRiQ12309.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati45 – 77HAT 1Add BLAST33
Repeati79 – 111HAT 2Add BLAST33
Repeati113 – 145HAT 3Add BLAST33
Repeati147 – 178HAT 4Add BLAST32
Repeati180 – 211HAT 5Add BLAST32
Repeati213 – 247HAT 6Add BLAST35
Repeati251 – 283HAT 7Add BLAST33
Repeati300 – 332HAT 8Add BLAST33
Repeati337 – 369HAT 9Add BLAST33
Repeati383 – 416HAT 10Add BLAST34
Repeati451 – 483HAT 11Add BLAST33
Repeati525 – 557HAT 12Add BLAST33
Repeati629 – 661HAT 13Add BLAST33

Sequence similaritiesi

Belongs to the crooked-neck family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00550000074931.
HOGENOMiHOG000207972.
InParanoidiQ12309.
KOiK12869.
OMAiFTFSKIW.
OrthoDBiEOG092C0UBN.

Family and domain databases

Gene3Di1.25.40.10. 5 hits.
InterProiView protein in InterPro
IPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
PfamiView protein in Pfam
PF02184. HAT. 1 hit.
SMARTiView protein in SMART
SM00386. HAT. 12 hits.
SUPFAMiSSF48452. SSF48452. 2 hits.

Sequencei

Sequence statusi: Complete.

Q12309-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDTLEPTAVD THVSAEQILR DVYKKGQKAR GSTNIDILDL EELREYQRRK
60 70 80 90 100
RTEYEGYLKR NRLDMGQWIR YAQFEIEQHD MRRARSIFER ALLVDSSFIP
110 120 130 140 150
LWIRYIDAEL KVKCINHARN LMNRAISTLP RVDKLWYKYL IVEESLNNVE
160 170 180 190 200
IVRSLYTKWC SLEPGVNAWN SFVDFEIRQK NWNGVREIYS KYVMAHPQMQ
210 220 230 240 250
TWLKWVRFEN RHGNTEFTRS VYSLAIDTVA NLQNLQIWSD MEVAKLVNSF
260 270 280 290 300
AHWEAAQQEY ERSSALYQIA IEKWPSNQLL KAGLLDFEKQ FGDINSIEET
310 320 330 340 350
ISYKRKMEYE TILSNNAYDY DTWWLYLDLI SESFPKQIMQ TFEKAIVDSR
360 370 380 390 400
PKELSKNVQW KRYIYLWMRY ICYVELELEN SLLEEELFQR LIDDIIPHKH
410 420 430 440 450
FTFSKIWLMY AKFLIRHDDV PKARKILGKA IGLCPKAKTF KGYIELEVKL
460 470 480 490 500
KEFDRVRKIY EKFIEFQPSD LQIWSQYGEL EENLGDWDRV RGIYTIALDE
510 520 530 540 550
NSDFLTKEAK IVLLQKYITF ETESQEFEKA RKLYRRYLEL NQYSPQSWIE
560 570 580 590 600
FAMYQTSTPT EQQLLDLAKL QSENVDEDIE FEITDENKLE ARKVFEEAIV
610 620 630 640 650
FFKEKDDKQG RLSILEALKD YEETYGTELD QETVKKRFPK VIKKVRLQNG
660 670 680
VEEEFVDYIF PDDIDDDKPK PSKFLELAKK WKQEQAL
Length:687
Mass (Da):82,445
Last modified:November 1, 1996 - v1
Checksum:iAE7D5EC5B3979E00
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X89514 Genomic DNA. Translation: CAA61696.1.
U53877 Genomic DNA. Translation: AAB82364.1.
Z73289 Genomic DNA. Translation: CAA97685.1.
BK006945 Genomic DNA. Translation: DAA09431.1.
PIRiS64954.
RefSeqiNP_013218.1. NM_001182004.1.

Genome annotation databases

EnsemblFungiiYLR117C; YLR117C; YLR117C.
GeneIDi850808.
KEGGisce:YLR117C.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiCLF1_YEAST
AccessioniPrimary (citable) accession number: Q12309
Secondary accession number(s): D6VYB5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: November 1, 1996
Last modified: July 5, 2017
This is version 134 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names