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Protein

Thioredoxin-like protein 4A

Gene

TXNL4A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes that are involved in spliceosome assembly.1 Publication

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • gene expression Source: Reactome
  • mitotic nuclear division Source: UniProtKB-KW
  • mRNA splicing, via spliceosome Source: Reactome
  • RNA splicing Source: Reactome
  • RNA splicing, via transesterification reactions Source: UniProtKB
  • spliceosomal complex assembly Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Cell cycle, Cell division, Mitosis, mRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Thioredoxin-like protein 4A
Alternative name(s):
DIM1 protein homolog
Spliceosomal U5 snRNP-specific 15 kDa protein
Thioredoxin-like U5 snRNP protein U5-15kD
Gene namesi
Name:TXNL4A
Synonyms:DIM1, TXNL4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 18

Organism-specific databases

HGNCiHGNC:30551. TXNL4A.

Subcellular locationi

GO - Cellular componenti

  • nucleoplasm Source: Reactome
  • spliceosomal complex Source: UniProtKB
  • U4/U6 x U5 tri-snRNP complex Source: GO_Central
  • U5 snRNP Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Involvement in diseasei

Burn-McKeown syndrome (BMKS)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disease characterized by choanal atresia, sensorineural deafness, cardiac defects, and typical craniofacial dysmorphism consisting of narrow palpebral fissures, coloboma of the lower eyelids, prominent nose with high nasal bridge, short philtrum, cleft lip and/or palate, and large and protruding ears. Intellectual development is normal.
See also OMIM:608572

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi38 – 381C → A: Viable when expressed in S.pombe. 1 Publication

Keywords - Diseasei

Deafness

Organism-specific databases

MalaCardsiTXNL4A.
MIMi608572. phenotype.
PharmGKBiPA134937290.

Polymorphism and mutation databases

BioMutaiTXNL4A.
DMDMi46577662.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 142142Thioredoxin-like protein 4APRO_0000218287Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi38 ↔ 792 Publications
Modified residuei132 – 1321PhosphoserineCombined sources

Post-translational modificationi

The disulfide bond seen in structures determined by X-ray crystallography (PubMed:10610776) and NMR (PubMed:12911302) is not essential for protein folding and function (PubMed:12911302 and PubMed:17467737).2 Publications

Keywords - PTMi

Disulfide bond, Phosphoprotein

Proteomic databases

EPDiP83876.
MaxQBiP83876.
PaxDbiP83876.
PRIDEiP83876.
TopDownProteomicsiP83876.

PTM databases

iPTMnetiP83876.
PhosphoSiteiP83876.

Expressioni

Gene expression databases

BgeeiP83876.
CleanExiHS_TXNL4A.
ExpressionAtlasiP83876. baseline and differential.
GenevisibleiP83876. HS.

Interactioni

Subunit structurei

Interacts with HNRPF, HNRPH2, NEDD9, ERBB4, and PQBP1. Component of the U5 snRNP complex. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39. Directly interacts with CD2BP2.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CD2BP2O954002EBI-746539,EBI-768015
EXOC5Q8IW243EBI-746539,EBI-10171392
LZTS2Q9BRK43EBI-746539,EBI-741037

Protein-protein interaction databases

BioGridi116113. 32 interactions.
IntActiP83876. 21 interactions.
MINTiMINT-1783239.
STRINGi9606.ENSP00000269601.

Structurei

Secondary structure

1
142
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi11 – 199Combined sources
Beta strandi22 – 3110Combined sources
Helixi36 – 5217Combined sources
Turni53 – 553Combined sources
Beta strandi56 – 627Combined sources
Turni63 – 653Combined sources
Turni68 – 714Combined sources
Beta strandi80 – 856Combined sources
Beta strandi88 – 936Combined sources
Beta strandi95 – 973Combined sources
Beta strandi102 – 1043Combined sources
Helixi109 – 12315Combined sources
Turni124 – 1263Combined sources
Beta strandi128 – 1314Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PQNNMR-A2-128[»]
1QGVX-ray1.40A1-142[»]
1SYXX-ray2.35A/C/E1-142[»]
3JCRelectron microscopy7.00E1-142[»]
4BWQX-ray2.10A/C/E/G4-137[»]
4BWSX-ray2.50A/D4-137[»]
4CDOX-ray2.50A/C4-137[»]
ProteinModelPortaliP83876.
SMRiP83876. Positions 4-137.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP83876.

Family & Domainsi

Sequence similaritiesi

Belongs to the DIM1 family.Curated

Phylogenomic databases

eggNOGiKOG3414. Eukaryota.
ENOG4111FE6. LUCA.
GeneTreeiENSGT00390000010779.
HOGENOMiHOG000198385.
HOVERGENiHBG053996.
InParanoidiP83876.
KOiK12859.
OMAiIRFGHDY.
OrthoDBiEOG79W97H.
PhylomeDBiP83876.
TreeFamiTF313562.

Family and domain databases

Gene3Di3.40.30.10. 1 hit.
InterProiIPR004123. Dim1.
IPR012336. Thioredoxin-like_fold.
[Graphical view]
PANTHERiPTHR12052. PTHR12052. 1 hit.
PfamiPF02966. DIM1. 1 hit.
[Graphical view]
PIRSFiPIRSF017199. mRNA_splic_U5. 1 hit.
SMARTiSM01410. DIM1. 1 hit.
[Graphical view]
SUPFAMiSSF52833. SSF52833. 1 hit.

Sequencei

Sequence statusi: Complete.

P83876-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSYMLPHLHN GWQVDQAILS EEDRVVVIRF GHDWDPTCMK MDEVLYSIAE
60 70 80 90 100
KVKNFAVIYL VDITEVPDFN KMYELYDPCT VMFFFRNKHI MIDLGTGNNN
110 120 130 140
KINWAMEDKQ EMVDIIETVY RGARKGRGLV VSPKDYSTKY RY
Length:142
Mass (Da):16,786
Last modified:April 26, 2004 - v1
Checksum:iEDDDAD7ADAEE87F3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF023611 mRNA. Translation: AAB81950.1.
AF146373 mRNA. Translation: AAF17332.1.
AK314901 mRNA. Translation: BAG37415.1.
CH471117 Genomic DNA. Translation: EAW66640.1.
BC001046 mRNA. Translation: AAH01046.1.
BC019272 mRNA. Translation: AAH19272.1.
CCDSiCCDS32852.1.
RefSeqiNP_001290400.1. NM_001303471.2.
NP_001292486.1. NM_001305557.1.
NP_001292492.1. NM_001305563.1.
NP_001292493.1. NM_001305564.1.
NP_006692.1. NM_006701.4.
UniGeneiHs.465498.

Genome annotation databases

EnsembliENST00000269601; ENSP00000269601; ENSG00000141759.
GeneIDi10907.
KEGGihsa:10907.
UCSCiuc002lnp.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF023611 mRNA. Translation: AAB81950.1.
AF146373 mRNA. Translation: AAF17332.1.
AK314901 mRNA. Translation: BAG37415.1.
CH471117 Genomic DNA. Translation: EAW66640.1.
BC001046 mRNA. Translation: AAH01046.1.
BC019272 mRNA. Translation: AAH19272.1.
CCDSiCCDS32852.1.
RefSeqiNP_001290400.1. NM_001303471.2.
NP_001292486.1. NM_001305557.1.
NP_001292492.1. NM_001305563.1.
NP_001292493.1. NM_001305564.1.
NP_006692.1. NM_006701.4.
UniGeneiHs.465498.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PQNNMR-A2-128[»]
1QGVX-ray1.40A1-142[»]
1SYXX-ray2.35A/C/E1-142[»]
3JCRelectron microscopy7.00E1-142[»]
4BWQX-ray2.10A/C/E/G4-137[»]
4BWSX-ray2.50A/D4-137[»]
4CDOX-ray2.50A/C4-137[»]
ProteinModelPortaliP83876.
SMRiP83876. Positions 4-137.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116113. 32 interactions.
IntActiP83876. 21 interactions.
MINTiMINT-1783239.
STRINGi9606.ENSP00000269601.

PTM databases

iPTMnetiP83876.
PhosphoSiteiP83876.

Polymorphism and mutation databases

BioMutaiTXNL4A.
DMDMi46577662.

Proteomic databases

EPDiP83876.
MaxQBiP83876.
PaxDbiP83876.
PRIDEiP83876.
TopDownProteomicsiP83876.

Protocols and materials databases

DNASUi10907.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000269601; ENSP00000269601; ENSG00000141759.
GeneIDi10907.
KEGGihsa:10907.
UCSCiuc002lnp.4. human.

Organism-specific databases

CTDi10907.
GeneCardsiTXNL4A.
HGNCiHGNC:30551. TXNL4A.
MalaCardsiTXNL4A.
MIMi608572. phenotype.
611595. gene.
neXtProtiNX_P83876.
PharmGKBiPA134937290.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3414. Eukaryota.
ENOG4111FE6. LUCA.
GeneTreeiENSGT00390000010779.
HOGENOMiHOG000198385.
HOVERGENiHBG053996.
InParanoidiP83876.
KOiK12859.
OMAiIRFGHDY.
OrthoDBiEOG79W97H.
PhylomeDBiP83876.
TreeFamiTF313562.

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

ChiTaRSiTXNL4A. human.
EvolutionaryTraceiP83876.
GeneWikiiTXNL4A.
GenomeRNAii10907.
NextBioi41427.
PROiP83876.
SOURCEiSearch...

Gene expression databases

BgeeiP83876.
CleanExiHS_TXNL4A.
ExpressionAtlasiP83876. baseline and differential.
GenevisibleiP83876. HS.

Family and domain databases

Gene3Di3.40.30.10. 1 hit.
InterProiIPR004123. Dim1.
IPR012336. Thioredoxin-like_fold.
[Graphical view]
PANTHERiPTHR12052. PTHR12052. 1 hit.
PfamiPF02966. DIM1. 1 hit.
[Graphical view]
PIRSFiPIRSF017199. mRNA_splic_U5. 1 hit.
SMARTiSM01410. DIM1. 1 hit.
[Graphical view]
SUPFAMiSSF52833. SSF52833. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Human homologue of the S. pombe Dim1p gene."
    Larin D., Ross B.M., Gilliam T.C.
    Submitted (SEP-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Liver.
  2. "Identification, characterization and crystal structure analysis of the human spliceosomal U5 snRNP-specific 15kD protein."
    Reuter K., Nottrott S., Fabrizio P., Luehrmann R., Ficner R.
    J. Mol. Biol. 294:515-525(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS), FUNCTION, DISULFIDE BOND, SUBUNIT.
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Cerebellum.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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: Lung.
  6. "Evidence that Dim1 associates with proteins involved in pre-mRNA splicing, and delineation of residues essential for Dim1 interactions with hnRNP F and Npw38/PQBP-1."
    Zhang Y.-Z., Lindblom T., Chang A., Sudol M., Sluder A.E., Golemis E.A.
    Gene 257:33-43(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HNRPF; HNRPH2; NEDD9 AND PQBP1, MUTAGENESIS.
  7. "The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP."
    Liu S., Rauhut R., Vornlocher H.-P., Luehrmann R.
    RNA 12:1418-1430(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-132, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  10. "Interactions of ErbB4 and Kap1 connect the growth factor and DNA damage response pathways."
    Gilmore-Hebert M., Ramabhadran R., Stern D.F.
    Mol. Cancer Res. 8:1388-1398(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH ERBB4, SUBCELLULAR LOCATION.
  11. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. Cited for: INVOLVEMENT IN BMKS.
  13. "The evolutionarily conserved Dim1 protein defines a novel branch of the thioredoxin fold superfamily."
    Zhang Y.-Z., Gould K.L., Dunbrack R.L. Jr., Cheng H., Roder H., Golemis E.A.
    Physiol. Genomics 1:109-118(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR, 3D-STRUCTURE MODELING, MUTAGENESIS OF CYS-38.
  14. "Structure, stability, and function of hDim1 investigated by NMR, circular dichroism, and mutational analysis."
    Zhang Y.Z., Cheng H., Gould K.L., Golemis E.A., Roder H.
    Biochemistry 42:9609-9618(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 1-128, CIRCULAR DICHROISM, DISULFIDE BOND, MUTAGENESIS.
  15. "Structural basis for the bifunctionality of the U5 snRNP 52K protein (CD2BP2)."
    Nielsen T.K., Liu S., Luhrmann R., Ficner R.
    J. Mol. Biol. 369:902-908(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH CD2BP2, INTERACTION WITH CD2BP2.
  16. "Mutations in the PQBP1 gene prevent its interaction with the spliceosomal protein U5-15 kD."
    Mizuguchi M., Obita T., Serita T., Kojima R., Nabeshima Y., Okazawa H.
    Nat. Commun. 5:3822-3822(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 4-137 IN COMPLEX WITH PQBP1 AND CD2BP2, INTERACTION WITH PQBP1 AND CD2BP2.

Entry informationi

Entry nameiTXN4A_HUMAN
AccessioniPrimary (citable) accession number: P83876
Secondary accession number(s): B2RC18, O14834
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: April 26, 2004
Last modified: May 11, 2016
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

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

Documents

  1. Human chromosome 18
    Human chromosome 18: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.