Reviewed, UniProtKB/Swiss-Prot Q13838 (UAP56_HUMAN)

Names and origin

Protein names

Recommended name:
    Spliceosome RNA helicase BAT1
    EC=3.6.1.-
Alternative name(s):
    DEAD box protein UAP56
    56 kDa U2AF65-associated protein
    ATP-dependent RNA helicase p47
    HLA-B-associated transcript-1

Gene names

Name:	BAT1
Synonyms:	UAP56

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	428 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has weak RNA-dependent ATPase activity. Required for mRNA export. Ref.9 Ref.10 Ref.15
Subunit structure	Homodimer, and heterodimer with DDX39. Component of the spliceosome. Interacts directly with U2AF2. Interacts directly with THOC4 and is necessary for THOC4 recruitment to spliced mRNA. Interacts with RBM8A, RNPS1 and SRRM1. Ref.9 Ref.10 Ref.11 Ref.12 Ref.16
Subcellular location	Nucleus. Ref.9 Ref.10 Ref.1
Sequence similarities	Belongs to the DEAD box helicase family. DECD subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.
Sequence caution	The sequence CAI17665.2 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Coding sequence diversity	Alternative splicing
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	mRNA export from nucleus Inferred from genetic interaction. Source: UniProtKB nuclear mRNA splicing, via spliceosome Inferred from genetic interaction. Source: UniProtKB
Cellular component	spliceosome Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent RNA helicase activity Ref.1 Traceable author statement. Source: ProtInc RNA binding Inferred from electronic annotation. Source: UniProtKB-KW identical protein binding Ref.12 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		1	EBI-348622,EBI-348622
C1orf77	Q9Y3Y2	1	EBI-348622,EBI-347794
DDX39	O00148	1	EBI-348622,EBI-348253
EXOSC9	Q06265	1	EBI-348622,EBI-347966
HCC1	P82979	1	EBI-348622,EBI-347495
HIPK2	Q9H2X6	1	EBI-348622,EBI-348345
HNRPLL	Q8WVV9	1	EBI-348622,EBI-535849
PIAS2	O75928	1	EBI-348622,EBI-348555
RPS15A	P62244	1	EBI-348622,EBI-347895
TDG	Q13569	1	EBI-348622,EBI-348333
THOC4	Q86V81	1	EBI-348622,EBI-347640
ZHX1	Q9UKY1	1	EBI-348622,EBI-347767

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q13838-1)

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.

Isoform 2 (identifier: Q13838-2)

The sequence of this isoform differs from the canonical sequence as follows:
     114-114: V → VYLGRVLGRGFWLGLV

Note: No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 428

428

Spliceosome RNA helicase BAT1

PRO_0000055071

Regions

Domain

76 – 249

174

Helicase ATP-binding

Domain

261 – 422

162

Helicase C-terminal

Nucleotide binding

89 – 96

8

ATP

Motif

45 – 73

29

Q motif

Motif

196 – 199

4

DECD box

Amino acid modifications

Modified residue

172

1

Phosphothreonine Ref.13

Natural variations

Alternative sequence

114

1

V → VYLGRVLGRGFWLGLV in isoform 2.

VSP_026347

Experimental info

Mutagenesis

198

1

C → A: No effect on ATPase activity. Ref.15

Sequence conflict

289

1

Q → R in BAD96632. Ref.3

Secondary structure

1

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428

Helix Strand Turn

Details...

Helix

54 – 62

9

Helix

70 – 80

11

Beta strand

85 – 88

4

Helix

95 – 106

12

Beta strand

116 – 119

4

Helix

123 – 136

14

Turn

137 – 139

3

Beta strand

145 – 149

5

Helix

154 – 163

10

Beta strand

167 – 171

5

Helix

173 – 181

9

Beta strand

192 – 197

6

Helix

198 – 202

5

Helix

205 – 216

12

Beta strand

220 – 229

10

Turn

233 – 235

3

Helix

236 – 240

5

Beta strand

247 – 250

4

Beta strand

263 – 268

6

Helix

271 – 273

3

Helix

274 – 284

11

Beta strand

288 – 293

6

Helix

297 – 309

13

Beta strand

314 – 317

4

Helix

323 – 334

12

Beta strand

339 – 345

7

Helix

353 – 355

3

Beta strand

357 – 363

7

Helix

368 – 378

11

Helix

380 – 382

3

Beta strand

386 – 391

6

Helix

394 – 407

14

Beta strand

411 – 413

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 7A55167BF576FB6F	FASTA	428	48,991
	10 20 30 40 50 60 MAENDVDNEL LDYEDDEVET AAGGDGAEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI 70 80 90 100 110 120 VDCGFEHPSE VQHECIPQAI LGMDVLCQAK SGMGKTAVFV LATLQQLEPV TGQVSVLVMC 130 140 150 160 170 180 HTRELAFQIS KEYERFSKYM PNVKVAVFFG GLSIKKDEEV LKKNCPHIVV GTPGRILALA 190 200 210 220 230 240 RNKSLNLKHI KHFILDECDK MLEQLDMRRD VQEIFRMTPH EKQVMMFSAT LSKEIRPVCR 250 260 270 280 290 300 KFMQDPMEIF VDDETKLTLH GLQQYYVKLK DNEKNRKLFD LLDVLEFNQV VIFVKSVQRC 310 320 330 340 350 360 IALAQLLVEQ NFPAIAIHRG MPQEERLSRY QQFKDFQRRI LVATNLFGRG MDIERVNIAF 370 380 390 400 410 420 NYDMPEDSDT YLHRVARAGR FGTKGLAITF VSDENDAKIL NDVQDRFEVN ISELPDEIDI SSYIEQTR
	Isoform 2. Checksum: 5B25C9C18CA433A4	FASTA	443	50,679
	10 20 30 40 50 60 MAENDVDNEL LDYEDDEVET AAGGDGAEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI 70 80 90 100 110 120 VDCGFEHPSE VQHECIPQAI LGMDVLCQAK SGMGKTAVFV LATLQQLEPV TGQVYLGRVL 130 140 150 160 170 180 GRGFWLGLVS VLVMCHTREL AFQISKEYER FSKYMPNVKV AVFFGGLSIK KDEEVLKKNC 190 200 210 220 230 240 PHIVVGTPGR ILALARNKSL NLKHIKHFIL DECDKMLEQL DMRRDVQEIF RMTPHEKQVM 250 260 270 280 290 300 MFSATLSKEI RPVCRKFMQD PMEIFVDDET KLTLHGLQQY YVKLKDNEKN RKLFDLLDVL 310 320 330 340 350 360 EFNQVVIFVK SVQRCIALAQ LLVEQNFPAI AIHRGMPQEE RLSRYQQFKD FQRRILVATN 370 380 390 400 410 420 LFGRGMDIER VNIAFNYDMP EDSDTYLHRV ARAGRFGTKG LAITFVSDEN DAKILNDVQD 430 440 RFEVNISELP DEIDISSYIE QTR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The BAT1 gene in the MHC encodes an evolutionarily conserved putative nuclear RNA helicase of the DEAD family." Peelman L., Chardon P., Nunes M., Renard C., Geffrotin C., Vaiman M., van Zeveren A., Coppieters W., van de Weghe A., Bouquet Y., Choy W., Strominger J., Spies T. Genomics 26:210-218(1995) [PubMed: 7601445] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION.
[2]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[3]	Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S. Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Kidney epithelium.
[4]	"Rapid evolution of major histocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity." Shiina T., Ota M., Shimizu S., Katsuyama Y., Hashimoto N., Takasu M., Anzai T., Kulski J.K., Kikkawa E., Naruse T., Kimura N., Yanagiya K., Watanabe A., Hosomichi K., Kohara S., Iwamoto C., Umehara Y., Meyer A. , Wanner V., Sano K., Macquin C., Ikeo K., Tokunaga K., Gojobori T., Inoko H., Bahram S. Genetics 173:1555-1570(2006) [PubMed: 16702430] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The DNA sequence and analysis of human chromosome 6." Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S. Nature 425:805-811(2003) [PubMed: 14574404] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Muscle.
[8]	"Homo sapiens BAT1 (BAT1) gene, partial cds; and PERB18 pseudogene, complete sequence." Allcock R.J.N., Price P., Gaudieri S., Leelayuwat C., Witt C.S., Dawkins R.L. Submitted (OCT-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 145-428.
[9]	"U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction." Fleckner J., Zhang M., Valcarcel J., Green M.R. Genes Dev. 11:1864-1872(1997) [PubMed: 9242493] [Abstract] Cited for: FUNCTION, INTERACTION WITH U2AF2 AND THE SPLICEOSOME, SUBCELLULAR LOCATION.
[10]	"Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly." Luo M.-J., Zhou Z., Magni K., Christoforides C., Rappsilber J., Mann M., Reed R. Nature 413:644-647(2001) [PubMed: 11675789] [Abstract] Cited for: FUNCTION, INTERACTION WITH THOC4 AND THE SPLICEOSOME, SUBCELLULAR LOCATION.
[11]	"An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation." McCracken S., Longman D., Johnstone I.L., Caceres J.F., Blencowe B.J. J. Biol. Chem. 278:44153-44160(2003) [PubMed: 12944400] [Abstract] Cited for: INTERACTION WITH RBM8A; RNPS1; SRRM1 AND THOC4.
[12]	"Analysis of a high-throughput yeast two-hybrid system and its use to predict the function of intracellular proteins encoded within the human MHC class III region." Lehner B., Semple J.I., Brown S.E., Counsell D., Campbell R.D., Sanderson C.M. Genomics 83:153-167(2004) [PubMed: 14667819] [Abstract] Cited for: HOMODIMERIZATION, INTERACTION WITH THOC4 AND DDX39.
[13]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-172, MASS SPECTROMETRY.
[14]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[15]	"Crystal structure of the human ATP-dependent splicing and export factor UAP56." Shi H., Cordin O., Minder C.M., Linder P., Xu R.-M. Proc. Natl. Acad. Sci. U.S.A. 101:17628-17633(2004) [PubMed: 15585580] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 44-428 IN COMPLEX WITH ADP, FUNCTION, MUTAGENESIS OF CYS-198.
[16]	"Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export." Zhao R., Shen J., Green M.R., MacMorris M., Blumenthal T. Structure 12:1373-1381(2004) [PubMed: 15296731] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 34-428, DIMERIZATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

Z37166 mRNA. Translation: CAA85523.1.
BT009909 mRNA. Translation: AAP88911.1.
AK222912 mRNA. Translation: BAD96632.1.
AB088115 Genomic DNA. Translation: BAC54953.1.
AB103621 Genomic DNA. Translation: BAF31287.1.
AB202112 Genomic DNA. Translation: BAE78637.1.
BA000025 Genomic DNA. Translation: BAB63306.1.
AL662847 Genomic DNA. Translation: CAI17664.2.
AL662847 Genomic DNA. Translation: CAI17665.2. Sequence problems.
AL662801 Genomic DNA. Translation: CAI18279.2.
AL662801 Genomic DNA. Translation: CAI18280.1.
AL662801 Genomic DNA. Translation: CAI18281.2.
AL662801 Genomic DNA. Translation: CAI18282.2.
AL662801 Genomic DNA. Translation: CAI18283.2.
BX001040 Genomic DNA. Translation: CAI18634.1.
BX248516 Genomic DNA. Translation: CAI41922.1.
BX927320 Genomic DNA. Translation: CAQ09974.1.
CR753820 Genomic DNA. Translation: CAQ07176.1.
CR753864 Genomic DNA. Translation: CAQ10634.1.
CH471081 Genomic DNA. Translation: EAX03404.1.
BC000361 mRNA. Translation: AAH00361.1.
BC013006 mRNA. Translation: AAH13006.1.
AF029061 Genomic DNA. Translation: AAB94615.1.
AF029062 Genomic DNA. Translation: AAC63046.1.

IPI

IPI00641829.
IPI00848161.

PIR

I37201.

RefSeq

NP_004631.1.
NP_542165.1.

UniGene

Hs.254042

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1T5I	X-ray	1.90	A	259-428	[»]
1T6N	X-ray	1.94	A/B	34-251	[»]
1XTI	X-ray	1.95	A	44-428	[»]
1XTJ	X-ray	2.70	A	44-423	[»]
1XTK	X-ray	2.40	A	45-428	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

Q13838. 17 interactions.

Protein family/group databases

TCDB

3.A.18.1.1. nuclear mRNA exporter (mRNA-E) family.

PTM databases

PhosphoSite

Q13838.

Proteomic databases

PRIDE

Q13838.

Genome annotation databases

Ensembl

ENSG00000198563. Homo sapiens. [Contig view]
ENSG00000215412. Homo sapiens. [Contig view]
ENSG00000215425. Homo sapiens. [Contig view]

GeneID

7919.

KEGG

hsa:7919.

UCSC

uc003ntt.1. human.

Organism-specific databases

GeneCards

GC06M031605.

H-InvDB

HIX0020115.
HIX0057729.
HIX0078590.

HGNC

HGNC:13917. BAT1.

MIM

142560. gene.

PharmGKB

PA25262.

GenAtlas

Search...

Phylogenomic databases

HOVERGEN

Q13838.

OMA

Q13838. ANAIREN.

Gene expression databases

CleanEx

HS_BAT1.

GermOnline

ENSG00000198563. Homo sapiens.

Family and domain databases

InterPro

IPR014001. DEAD-like_N.
IPR001650. DNA/RNA_helicase_C.
IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014021. Helicase_SF1/SF2_ATP-bd.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]

Pfam

PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]

SMART

SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]

PROSITE

PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

30405.

SOURCE

Search...

Entry information

Entry name

UAP56_HUMAN

Accession

Primary (citable) accession number: Q13838
Secondary accession number(s): B0S8C0 , O43496, Q0EFA1, Q2L6F9, Q53GL9, Q5RJ64, Q5RJ66, Q5ST94, Q5STB4, Q5STB5, Q5STB7, Q5STB8, Q5STU4, Q5STU5, Q5STU6, Q5STU8, Q71V76

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	July 7, 2009
This is version 96 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)