Reviewed, UniProtKB/Swiss-Prot Q9UJV9 (DDX41_HUMAN)

Names and origin

Protein names

Recommended name:
    Probable ATP-dependent RNA helicase DDX41
    EC=3.6.1.-
Alternative name(s):
    DEAD box protein 41
    DEAD box protein abstrakt homolog

Gene names

Name:	DDX41
Synonyms:	ABS

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	622 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Probable ATP-dependent RNA helicase. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing.
Subunit structure	Identified in the spliceosome C complex, at least composed of AQR, C19orf29, CDC40, CDC5L, CRNKL1, DDX23, DDX41, DDX48, DDX5, DGCR14, DHX35, DHX38, DHX8, EFTUD2, FRG1, GPATC1, HNRPA1, HNRPA2B1, HNRPA3, HNRPC, HNRPF, HNRPH1, HNRPK, HNRPM, HNRPR, HNRPU, KIAA1160, KIAA1604, LSM2, LSM3, MAGOH, MORG1, PABPC1, PLRG1, PNN, PPIE, PPIL1, PPIL3, PPWD1, PRPF19, PRPF4B, PRPF6, PRPF8, RALY, RBM22, RBM8A, RBMX, SART1, SF3A1, SF3A2, SF3A3, SF3B1, SF3B2, SF3B3, SFRS1, SKIV2L2, SNRNP200, SNRNP40, SNRPA1, SNRPB, SNRPB2, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, SNW1, SRRM1, SRRM2, SYF2, SYNCRIP, TFIP11, THOC4, U2AF1, XAB2 and ZCCHC8.
Subcellular location	Nucleus Potential.
Sequence similarities	Belongs to the DEAD box helicase family. DDX41 subfamily. Contains 1 CCHC-type zinc finger. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.
Sequence caution	The sequence CAE46035.1 differs from that shown. Reason: Miscellaneous discrepancy. Intron retention.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Domain	Zinc-finger
Ligand	ATP-binding Metal-binding Nucleotide-binding RNA-binding Zinc
Molecular function	Helicase Hydrolase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	RNA splicing Inferred from electronic annotation. Source: UniProtKB-KW apoptosis Ref.1 Traceable author statement. Source: ProtInc mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW multicellular organismal development Ref.1 Traceable author statement. Source: ProtInc
Cellular component	spliceosomal complex Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro RNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ABL1	P00519	1	EBI-1046350,EBI-375543
CRK	P46108	1	EBI-1046350,EBI-886
FYN	P06241	1	EBI-1046350,EBI-515315
RNPS1	Q15287	1	EBI-1046350,EBI-395959

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 622

622

Probable ATP-dependent RNA helicase DDX41

PRO_0000054970

Regions

Domain

212 – 396

185

Helicase ATP-binding

Domain

407 – 567

161

Helicase C-terminal

Nucleotide binding

225 – 232

8

ATP By similarity

Zinc finger

580 – 597

18

CCHC-type

Motif

181 – 209

29

Q motif

Motif

344 – 347

4

DEAD box

Amino acid modifications

Modified residue

21

1

Phosphoserine Ref.7 Ref.8 Ref.11 Ref.13 Ref.14

Modified residue

23

1

Phosphoserine Ref.7 Ref.8 Ref.11 Ref.13 Ref.14 Ref.9 Ref.10

Experimental info

Sequence conflict

17 – 43

27

PAGGS…LRQRR → LPEEAAPRRKMRTTRTTCPM CRYAAP in AAF04150. Ref.1

Sequence conflict

56

1

K → E in BAA91585. Ref.2

Sequence conflict

64

1

Q → E in BAB55355. Ref.2

Sequence conflict

165

1

K → E in BAB55355. Ref.2

Sequence conflict

191

1

A → T in BAA91585. Ref.2

Sequence conflict

352

1

M → T in BAA91585. Ref.2

Sequence conflict

552

1

L → Q in BAB55355. Ref.2

Sequence conflict

570

1

D → G in CAE46035. Ref.5

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

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.

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.

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.

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.

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622

Helix Strand Turn

Details...

Beta strand

408 – 414

7

Helix

417 – 419

3

Helix

420 – 428

9

Beta strand

435 – 438

4

Helix

442 – 455

14

Beta strand

459 – 462

4

Helix

468 – 480

13

Beta strand

484 – 488

5

Helix

490 – 493

4

Beta strand

502 – 508

7

Helix

513 – 520

8

Beta strand

531 – 536

6

Helix

542 – 554

13

Helix

561 – 564

4

Sequences

	Sequence		Length	Mass (Da)
	Q9UJV9-1 [UniParc]. Last modified May 10, 2002. Version 2. Checksum: E0A328724E0DF99A	FASTA	622	69,838
	10 20 30 40 50 60 MEESEPERKR ARTDEVPAGG SRSEAEDEDD EDYVPYVPLR QRRQLLLQKL LQRRRKGAAE 70 80 90 100 110 120 EEQQDSGSEP RGDEDDIPLG PQSNVSLLDQ HQHLKEKAEA RKESAKEKQL KEEEKILESV 130 140 150 160 170 180 AEGRALMSVK EMAKGITYDD PIKTSWTPPR YVLSMSEERH ERVRKKYHIL VEGDGIPPPI 190 200 210 220 230 240 KSFKEMKFPA AILRGLKKKG IHHPTPIQIQ GIPTILSGRD MIGIAFTGSG KTLVFTLPVI 250 260 270 280 290 300 MFCLEQEKRL PFSKREGPYG LIICPSRELA RQTHGILEYY CRLLQEDSSP LLRCALCIGG 310 320 330 340 350 360 MSVKEQMETI RHGVHMMVAT PGRLMDLLQK KMVSLDICRY LALDEADRMI DMGFEGDIRT 370 380 390 400 410 420 IFSYFKGQRQ TLLFSATMPK KIQNFAKSAL VKPVTINVGR AGAASLDVIQ EVEYVKEEAK 430 440 450 460 470 480 MVYLLECLQK TPPPVLIFAE KKADVDAIHE YLLLKGVEAV AIHGGKDQEE RTKAIEAFRE 490 500 510 520 530 540 GKKDVLVATD VASKGLDFPA IQHVINYDMP EEIENYVHRI GRTGRSGNTG IATTFINKAC 550 560 570 580 590 600 DESVLMDLKA LLLEAKQKVP PVLQVLHCGD ESMLDIGGER GCAFCGGLGH RITDCPKLEA 610 620 MQTKQVSNIG RKDYLAHSSM DF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Developmental and cell biological functions of the Drosophila DEAD-box protein abstrakt." Irion U., Leptin M. Curr. Biol. 9:1373-1381(1999) [PubMed: 10607561] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"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: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Placenta.
[3]	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].
[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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Skin.
[5]	"The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed: 17974005] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 47-622. Tissue: Amygdala.
[6]	"Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis." Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J. RNA 8:426-439(2002) [PubMed: 11991638] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPICEOSOMAL C COMPLEX.
[7]	"Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-21 AND SER-23, MASS SPECTROMETRY. Tissue: Epithelium.
[8]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed: 17081983] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-21 AND SER-23, MASS SPECTROMETRY. Tissue: Epithelium.
[9]	"Phosphoproteome analysis of the human mitotic spindle." Nousiainen M., Sillje H.H.W., Sauer G., Nigg E.A., Koerner R. Proc. Natl. Acad. Sci. U.S.A. 103:5391-5396(2006) [PubMed: 16565220] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-23, MASS SPECTROMETRY. Tissue: Epithelium.
[10]	"Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis." Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III J. Proteome Res. 7:1346-1351(2008) [PubMed: 18220336] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-23, MASS SPECTROMETRY.
[11]	"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 SER-21 AND SER-23, MASS SPECTROMETRY.
[12]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[13]	"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-21 AND SER-23, MASS SPECTROMETRY.
[14]	"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: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-21 AND SER-23, MASS SPECTROMETRY. Tissue: T-cell.
[15]	"Human dead-box RNA helicase DDX41." Structural genomics consortium (SGC) Submitted (APR-2007) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 402-569.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF195417 mRNA. Translation: AAF04150.1.
AK001255 mRNA. Translation: BAA91585.1.
AK027768 mRNA. Translation: BAB55355.1.
AK315491 mRNA. Translation: BAG37875.1.
CH471195 Genomic DNA. Translation: EAW84981.1.
BC015476 mRNA. Translation: AAH15476.1.
AL137455 mRNA. Translation: CAB70746.1.
BX641072 mRNA. Translation: CAE46035.1. Sequence problems.

IPI

IPI00007208.

PIR

T46269.

RefSeq

NP_057306.2.

UniGene

Hs.484288

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2P6N	X-ray	2.60	A/B	402-569	[»]

SMR

Q9UJV9. Positions 160-399, 169-564.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9UJV9. 4 interactions.

STRING

Q9UJV9.

PTM databases

PhosphoSite

Q9UJV9.

Proteomic databases

PeptideAtlas

Q9UJV9.

PRIDE

Q9UJV9.

Genome annotation databases

Ensembl

ENST00000330503; ENSP00000330349; ENSG00000183258; Homo sapiens. [Genome view]

GeneID

51428.

KEGG

hsa:51428.

UCSC

uc003mho.1. human.

Organism-specific databases

CTD

51428.

GeneCards

GC05M176871.

HGNC

HGNC:18674. DDX41.

HPA

HPA017911.

MIM

608170. gene.

PharmGKB

PA134908862.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

HBG737336.

HOVERGEN

Q9UJV9.

InParanoid

Q9UJV9.

OMA

MGFEEDV.

OrthoDB

EOG9NCQ02.

PhylomeDB

Q9UJV9.

Gene expression databases

ArrayExpress

Q9UJV9.

Bgee

Q9UJV9.

CleanEx

HS_DDX41.

Genevestigator

Q9UJV9.

GermOnline

ENSG00000183258. 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.
IPR001878. Znf_CCHC.
[Graphical view]

Pfam

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

SMART

SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SM00343. ZnF_C2HC. 1 hit.
[Graphical view]

PROSITE

PS00039. DEAD_ATP_HELICASE. False negative.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
PS50158. ZF_CCHC. False negative.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

54987.

SOURCE

Search...

Entry information

Entry name

DDX41_HUMAN

Accession

Primary (citable) accession number: Q9UJV9
Secondary accession number(s): B2RDC8 , Q96BK6, Q96K05, Q9NT96, Q9NW04

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 2000
Last sequence update:	May 10, 2002
Last modified:	January 19, 2010
This is version 102 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

Disclaimer

Any 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.