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Protein

Transcription factor A, mitochondrial

Gene

Tfam

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Isoform Mitochondrial binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. Required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. Promotes transcription initiation from the HSP1 and the light strand promoter by binding immediately upstream of transcriptional start sites. Is able to unwind DNA. Bends the mitochondrial light strand promoter DNA into a U-turn shape via its HMG boxes. Required for maintenance of normal levels of mitochondrial DNA. May play a role in organizing and compacting mitochondrial DNA (By similarity). Isoform Nuclear may also function as a transcriptional activator or may have a structural role in the compaction of nuclear DNA during spermatogenesis (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei57 – 571Intercalates between bases and promotes DNA bendingBy similarity
Sitei181 – 1811Intercalates between bases and promotes DNA bendingBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi49 – 11769HMG box 1PROSITE-ProRule annotationAdd
BLAST
DNA bindingi154 – 21865HMG box 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • chromatin binding Source: UniProtKB
  • DNA binding Source: RGD
  • DNA binding, bending Source: UniProtKB
  • heat shock protein binding Source: RGD
  • mitochondrial light strand promoter sense binding Source: UniProtKB
  • poly(A) RNA binding Source: Ensembl
  • RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: Ensembl
  • transcription coactivator binding Source: RGD
  • transcription factor activity, sequence-specific DNA binding Source: RGD

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-RNO-163282. Mitochondrial transcription initiation.
R-RNO-2151201. Transcriptional activation of mitochondrial biogenesis.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription factor A, mitochondrial
Short name:
mtTFA
Gene namesi
Name:Tfam
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 20

Organism-specific databases

RGDi620682. Tfam.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • mitochondrial matrix Source: Reactome
  • mitochondrial nucleoid Source: UniProtKB
  • mitochondrion Source: RGD
  • nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Mitochondrion nucleoid, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 4242MitochondrionSequence analysisAdd
BLAST
Chaini43 – 244202Transcription factor A, mitochondrialPRO_0000013472Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei54 – 541Phosphoserine; by PKABy similarity
Modified residuei55 – 551Phosphoserine; by PKABy similarity
Modified residuei60 – 601Phosphoserine; by PKABy similarity
Modified residuei66 – 661N6-succinyllysineBy similarity
Modified residuei159 – 1591Phosphoserine; by PKABy similarity
Modified residuei192 – 1921PhosphoserineBy similarity

Post-translational modificationi

Phosphorylation by PKA within the HMG box 1 impairs DNA binding and promotes degradation by the AAA+ Lon protease.By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ91ZW1.
PRIDEiQ91ZW1.

Expressioni

Tissue specificityi

The mitochondrial isoform is widely expressed while the nuclear isoform is testis-specific.

Gene expression databases

GenevisibleiQ91ZW1. RN.

Interactioni

Subunit structurei

Monomer; binds DNA as a monomer. Interacts with TFB1M and TFB2M. Interacts with CLPX; this enhances DNA-binding (By similarity).By similarity

GO - Molecular functioni

  • heat shock protein binding Source: RGD
  • transcription coactivator binding Source: RGD

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000000753.

Structurei

3D structure databases

ProteinModelPortaliQ91ZW1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

Binds DNA via its HMG boxes. When bound to the mitochondrial light strand promoter, bends DNA into a U-turn shape, each HMG box bending the DNA by 90 degrees (By similarity).By similarity

Sequence similaritiesi

Contains 2 HMG box DNA-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Transit peptide

Phylogenomic databases

eggNOGiKOG0381. Eukaryota.
COG5648. LUCA.
GeneTreeiENSGT00440000039001.
HOGENOMiHOG000139423.
HOVERGENiHBG106674.
InParanoidiQ91ZW1.
KOiK11830.
OMAiKWTRLSD.
OrthoDBiEOG7CG724.
PhylomeDBiQ91ZW1.
TreeFamiTF318343.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
[Graphical view]
PfamiPF00505. HMG_box. 1 hit.
PF09011. HMG_box_2. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 2 hits.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 2 hits.
PROSITEiPS50118. HMG_BOX_2. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

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

Isoform Mitochondrial (identifier: Q91ZW1-1) [UniParc]FASTAAdd to basket

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
MALFRGMWGV LRTLGRTGVE MCAGCGGRIP SPVSLICIPK CFSSLGNYPK
60 70 80 90 100
KPMSSYLRFS TEQLPKFKAK HPDAKVSELI RKIAAMWREL PEAEKKVYEA
110 120 130 140 150
DFKAEWKVYK EAVSKYKEQL TPSQLMGLEK EARQKRLKKK AQIKRRELIL
160 170 180 190 200
LGKPKRPRSA YNIYVSESFQ EAKDESAQGK LKLVNQAWKN LSHDEKQAYI
210 220 230 240
QLAKDDRIRY DNEMKSWEEQ MAEVGRSDLI RRSVKRPPGD ISEN
Length:244
Mass (Da):28,187
Last modified:December 1, 2001 - v1
Checksum:i8725027A6331D62E
GO
Isoform Nuclear (identifier: Q91ZW1-2)

Sequence is not available
Length:
Mass (Da):

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti171 – 1711E → G in BAA77755 (PubMed:10902920).Curated
Sequence conflicti177 – 1771A → P in BAA77755 (PubMed:10902920).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB014089 mRNA. Translation: BAA77755.1.
AJ312746 mRNA. Translation: CAC84763.1.
AF377866 mRNA. Translation: AAL12892.1.
BC062022 mRNA. Translation: AAH62022.1.
RefSeqiNP_112616.1. NM_031326.1.
UniGeneiRn.18266.

Genome annotation databases

EnsembliENSRNOT00000000753; ENSRNOP00000000753; ENSRNOG00000000613. [Q91ZW1-1]
GeneIDi83474.
KEGGirno:83474.
UCSCiRGD:620682. rat. [Q91ZW1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB014089 mRNA. Translation: BAA77755.1.
AJ312746 mRNA. Translation: CAC84763.1.
AF377866 mRNA. Translation: AAL12892.1.
BC062022 mRNA. Translation: AAH62022.1.
RefSeqiNP_112616.1. NM_031326.1.
UniGeneiRn.18266.

3D structure databases

ProteinModelPortaliQ91ZW1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000000753.

Proteomic databases

PaxDbiQ91ZW1.
PRIDEiQ91ZW1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000000753; ENSRNOP00000000753; ENSRNOG00000000613. [Q91ZW1-1]
GeneIDi83474.
KEGGirno:83474.
UCSCiRGD:620682. rat. [Q91ZW1-1]

Organism-specific databases

CTDi7019.
RGDi620682. Tfam.

Phylogenomic databases

eggNOGiKOG0381. Eukaryota.
COG5648. LUCA.
GeneTreeiENSGT00440000039001.
HOGENOMiHOG000139423.
HOVERGENiHBG106674.
InParanoidiQ91ZW1.
KOiK11830.
OMAiKWTRLSD.
OrthoDBiEOG7CG724.
PhylomeDBiQ91ZW1.
TreeFamiTF318343.

Enzyme and pathway databases

ReactomeiR-RNO-163282. Mitochondrial transcription initiation.
R-RNO-2151201. Transcriptional activation of mitochondrial biogenesis.

Miscellaneous databases

PROiQ91ZW1.

Gene expression databases

GenevisibleiQ91ZW1. RN.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
[Graphical view]
PfamiPF00505. HMG_box. 1 hit.
PF09011. HMG_box_2. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 2 hits.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 2 hits.
PROSITEiPS50118. HMG_BOX_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation of rat mitochondrial transcription factor A (r-Tfam) cDNA."
    Inagaki H., Hayashi T., Matsushima Y., Lin K.H., Maeda S., Ichihara S., Hitagawa Y., Saito T.
    DNA Seq. 11:131-135(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], ALTERNATIVE SPLICING.
    Strain: Sprague-Dawley.
    Tissue: Brain.
  2. "Characterization of the mtTFA gene and identification of a processed pseudogene in rat."
    Mezzina M., Reyes A., D'Errico I., Gadaleta G.
    Gene 286:105-112(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Sprague-Dawley.
  3. "Mitochondrial transcription factor A and its downstream targets are up-regulated in a rat hepatoma."
    Dong X., Ghoshal K., Majumder S., Yadav S.P., Jacob S.T.
    J. Biol. Chem. 277:43309-43318(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: ACI.
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Prostate.

Entry informationi

Entry nameiTFAM_RAT
AccessioniPrimary (citable) accession number: Q91ZW1
Secondary accession number(s): Q9WTM7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2002
Last sequence update: December 1, 2001
Last modified: June 8, 2016
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.