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Protein

Transcription factor IIIA

Gene

gtf3a

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts as both a positive transcription factor for 5S RNA genes and a specific RNA binding protein that complexes with 5S RNA in oocytes to form the 7S ribonucleoprotein storage particle. May play an essential role in the developmental change in 5S RNA gene expression. Interacts with the internal control region (ICR) of approximately 50 bases within the 5S RNA genes, is required for correct transcription of these genes by RNA polymerase III. Also binds the transcribed 5S RNA's.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri35 – 5925C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri65 – 8925C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri95 – 12026C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri127 – 15125C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri157 – 18125C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri184 – 21027C2H2-type 6PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri214 – 23623C2H2-type 7PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri243 – 26826C2H2-type 8PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri274 – 29825C2H2-type 9PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription factor IIIA
Short name:
TFIIIA
Alternative name(s):
S-TFIIIA/O-TFIIIA
Gene namesi
Name:gtf3a
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-6252591. gtf3a.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi38 – 381S → E or A: Abolishes phosphorylation by CK2. 1 Publication
Mutagenesisi42 – 421C → S: Loss of DNA binding. 1 Publication
Mutagenesisi55 – 551H → L: Inhibition of specific DNA binding. 1 Publication
Mutagenesisi91 – 911G → S: Loss of DNA binding. 1 Publication
Mutagenesisi93 – 931K → E: Loss of DNA binding. 1 Publication
Mutagenesisi134 – 1341C → S: No effect. 1 Publication
Mutagenesisi186 – 1861C → S: No effect. 1 Publication
Mutagenesisi336 – 3361S → E or A: Slightly decreases phosphorylation by CK2. 1 Publication
Mutagenesisi350 – 3501S → E or A: No effect on phosphorylation by CK2. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 366366Transcription factor IIIAPRO_0000041632Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei38 – 381Phosphoserine; by CK21 Publication
Modified residuei336 – 3361Phosphoserine; by CK2; in vitro1 Publication

Post-translational modificationi

The N-terminus is blocked.

Keywords - PTMi

Phosphoprotein

PTM databases

iPTMnetiP03001.

Expressioni

Tissue specificityi

Synthesized in oocytes and, in much lower levels, in somatic cells.

Developmental stagei

The levels follow the transcriptional activity of oocyte type 5S RNA genes during embryogenesis, present in very high levels in maturing oocytes when oocyte type 5S genes are being expressed, and in much lower levels in somatic cells where the oocyte type genes are not expressed.

Structurei

Secondary structure

1
366
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi38 – 414Combined sources
Beta strandi45 – 484Combined sources
Helixi49 – 6012Combined sources
Beta strandi64 – 663Combined sources
Beta strandi75 – 784Combined sources
Helixi79 – 868Combined sources
Turni87 – 915Combined sources
Beta strandi99 – 1013Combined sources
Beta strandi105 – 1073Combined sources
Helixi109 – 1179Combined sources
Turni122 – 1243Combined sources
Beta strandi131 – 1344Combined sources
Beta strandi137 – 1404Combined sources
Helixi141 – 15212Combined sources
Beta strandi156 – 1583Combined sources
Beta strandi161 – 1633Combined sources
Beta strandi167 – 1704Combined sources
Helixi171 – 18212Combined sources
Beta strandi183 – 1853Combined sources
Turni189 – 1913Combined sources
Beta strandi195 – 1984Combined sources
Helixi199 – 20810Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TF3NMR-A32-123[»]
1TF6X-ray3.10A/D23-212[»]
1UN6X-ray3.10B/C/D127-212[»]
2HGHNMR-A127-212[»]
2J7JX-ray1.65A127-210[»]
ProteinModelPortaliP03001.
SMRiP03001. Positions 29-210.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03001.

Family & Domainsi

Sequence similaritiesi

Contains 9 C2H2-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri35 – 5925C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri65 – 8925C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri95 – 12026C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri127 – 15125C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri157 – 18125C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri184 – 21027C2H2-type 6PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri214 – 23623C2H2-type 7PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri243 – 26826C2H2-type 8PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri274 – 29825C2H2-type 9PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

HOVERGENiHBG017915.
KOiK09191.

Family and domain databases

Gene3Di3.30.160.60. 9 hits.
InterProiIPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 9 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 8 hits.
PS50157. ZINC_FINGER_C2H2_2. 7 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative initiation. AlignAdd to basket

Isoform Somatic (identifier: P03001-1) [UniParc]FASTAAdd to basket

Also known as: S-TFIIIA

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAAKVASTSS EEAEGSLVTE GEMGEKALPV VYKRYICSFA DCGAAYNKNW
60 70 80 90 100
KLQAHLCKHT GEKPFPCKEE GCEKGFTSLH HLTRHSLTHT GEKNFTCDSD
110 120 130 140 150
GCDLRFTTKA NMKKHFNRFH NIKICVYVCH FENCGKAFKK HNQLKVHQFS
160 170 180 190 200
HTQQLPYECP HEGCDKRFSL PSRLKRHEKV HAGYPCKKDD SCSFVGKTWT
210 220 230 240 250
LYLKHVAECH QDLAVCDVCN RKFRHKDYLR DHQKTHEKER TVYLCPRDGC
260 270 280 290 300
DRSYTTAFNL RSHIQSFHEE QRPFVCEHAG CGKCFAMKKS LERHSVVHDP
310 320 330 340 350
EKRKLKEKCP RPKRSLASRL TGYIPPKSKE KNASVSGTEK TDSLVKNKPS
360
GTETNGSLVL DKLTIQ
Length:366
Mass (Da):41,911
Last modified:July 15, 1998 - v2
Checksum:i29237E710292FA24
GO
Isoform Oocyte (identifier: P03001-2) [UniParc]FASTAAdd to basket

Also known as: O-TFIIIA

The sequence of this isoform differs from the canonical sequence as follows:
     1-22: Missing.

Show »
Length:344
Mass (Da):39,746
Checksum:i8ACFE717EA8A1322
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti4 – 41K → T in CAA33786 (PubMed:2744458).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti96 – 961T → K.
Natural varianti319 – 3191R → C.
Natural varianti335 – 3351V → I.
Natural varianti356 – 3561G → D.
Natural varianti365 – 3651I → L.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 2222Missing in isoform Oocyte. CuratedVSP_018962Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02938 mRNA. Translation: AAA49967.1.
X03681
, X03735, X03736, X03737, X03738, X03739 Genomic DNA. Translation: CAB51745.1.
X15785 Genomic DNA. Translation: CAA33786.1.
PIRiA35916.
A90857. TWXL3.
RefSeqiNP_001081328.1. NM_001087859.1. [P03001-2]
UniGeneiXl.860.

Genome annotation databases

GeneIDi397777.
KEGGixla:397777.

Keywords - Coding sequence diversityi

Alternative initiation, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02938 mRNA. Translation: AAA49967.1.
X03681
, X03735, X03736, X03737, X03738, X03739 Genomic DNA. Translation: CAB51745.1.
X15785 Genomic DNA. Translation: CAA33786.1.
PIRiA35916.
A90857. TWXL3.
RefSeqiNP_001081328.1. NM_001087859.1. [P03001-2]
UniGeneiXl.860.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TF3NMR-A32-123[»]
1TF6X-ray3.10A/D23-212[»]
1UN6X-ray3.10B/C/D127-212[»]
2HGHNMR-A127-212[»]
2J7JX-ray1.65A127-210[»]
ProteinModelPortaliP03001.
SMRiP03001. Positions 29-210.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

iPTMnetiP03001.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi397777.
KEGGixla:397777.

Organism-specific databases

CTDi2971.
XenbaseiXB-GENE-6252591. gtf3a.

Phylogenomic databases

HOVERGENiHBG017915.
KOiK09191.

Miscellaneous databases

EvolutionaryTraceiP03001.

Family and domain databases

Gene3Di3.30.160.60. 9 hits.
InterProiIPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 9 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 8 hits.
PS50157. ZINC_FINGER_C2H2_2. 7 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Xenopus 5S gene transcription factor, TFIIIA: characterization of a cDNA clone and measurement of RNA levels throughout development."
    Ginsberg A.M., King B.O., Roeder R.G.
    Cell 39:479-489(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 23-366.
  2. "Structure of the gene for Xenopus transcription factor TFIIIA."
    Yun Tso J., van den Berg J., Korn L.J.
    Nucleic Acids Res. 14:2187-2201(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 23-366.
  3. "The developmental expression of the gene for TFIIIA in Xenopus laevis."
    Taylor W., Jackson I.J., Siegel N., Kumar A., Brown D.D.
    Nucleic Acids Res. 14:6185-6195(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE, PROTEIN SEQUENCE OF 112-137.
  4. "Positive and negative regulation of the gene for transcription factor IIIA in Xenopus laevis oocytes."
    Scotto K.W., Kaulen H., Roeder R.G.
    Genes Dev. 3:651-662(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-35.
  5. "The characterization of the TFIIIA synthesized in somatic cells of Xenopus laevis."
    Kim S.H., Darby M.K., Joho K.E., Brown D.D.
    Genes Dev. 4:1602-1610(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-26.
  6. "Specific interaction of the first three zinc fingers of TFIIIA with the internal control region of the Xenopus 5 S RNA gene."
    Liao X.B., Clemens K.R., Tennant L., Wright P.E., Gottesfeld J.M.
    J. Mol. Biol. 223:857-871(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 23-123.
  7. "Structural elements in the N-terminal half of transcription factor IIIA required for factor binding to the 5S RNA gene internal control region."
    Smith J.F., Hawkins J., Leonard R.E., Hanas J.S.
    Nucleic Acids Res. 19:6871-6876(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF CYS-42; HIS-55; GLY-91; LYS-93; CYS-134 AND CYS-186.
  8. "Phosphorylation of Xenopus transcription factor IIIA by an oocyte protein kinase CK2."
    Westmark C.J., Ghose R., Huber P.W.
    Biochem. J. 362:375-382(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-38 AND SER-336, MUTAGENESIS OF SER-38; SER-336 AND SER-350.
  9. "Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes."
    Miller J., McLachlan A.D., Klug A.
    EMBO J. 4:1609-1614(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: REPEATS ANALYSIS.
  10. "The primary structure of transcription factor TFIIIA has 12 consecutive repeats."
    Brown R.S., Sander C., Argos P.
    FEBS Lett. 186:271-274(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: REPEATS ANALYSIS.
  11. "Multiple internal repeats within the structure of the 5S RNA/DNA binding transcription factor TF-IIIA from Xenopus laevis."
    Boehm S., Drescher B.
    Studia Biophys. 107:237-247(1985)
    Cited for: REPEATS ANALYSIS.
  12. "Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA."
    Foster M.P., Wuttke D.S., Radhakrishnan I., Case D.A., Gottesfeld J.M., Wright P.E.
    Nat. Struct. Biol. 4:605-608(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 10-101.
  13. "Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex."
    Nolte R.T., Conlin R.M., Harrison S.C., Brown R.S.
    Proc. Natl. Acad. Sci. U.S.A. 95:2938-2943(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 32-210.

Entry informationi

Entry nameiTF3A_XENLA
AccessioniPrimary (citable) accession number: P03001
Secondary accession number(s): Q91856
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 15, 1998
Last modified: January 20, 2016
This is version 129 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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.