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Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.4.13) (Helicase CA8)

 PRP28_YEAST             Reviewed;         588 AA.
P23394; D6VSM3; P20450;
01-NOV-1991, integrated into UniProtKB/Swiss-Prot.
01-NOV-1995, sequence version 2.
23-MAY-2018, entry version 178.
RecName: Full=Pre-mRNA-splicing ATP-dependent RNA helicase PRP28;
EC=3.6.4.13;
AltName: Full=Helicase CA8;
Name=PRP28; OrderedLocusNames=YDR243C; ORFNames=YD8419.10C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND MUTAGENESIS OF
GLY-297.
STRAIN=YJJ48;
PubMed=2010088; DOI=10.1101/gad.5.4.629;
Strauss E.J., Guthrie C.;
"A cold-sensitive mRNA splicing mutant is a member of the RNA helicase
gene family.";
Genes Dev. 5:629-641(1991).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169867;
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N.,
Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M.,
Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L.,
Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M.,
Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S.,
Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M.,
Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S.,
Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K.,
Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D.,
Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C.,
Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T.,
Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E.,
Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W.,
Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K.,
Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S.,
Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A.,
Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S.,
Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M.,
Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y.,
Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M.,
Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E.,
Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R.,
Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
Mewes H.-W., Zollner A., Zaccaria P.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
Nature 387:75-78(1997).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 339-526.
PubMed=2406722; DOI=10.1073/pnas.87.4.1571;
Chang T.-H., Arenas J., Abelson J.;
"Identification of five putative yeast RNA helicase genes.";
Proc. Natl. Acad. Sci. U.S.A. 87:1571-1575(1990).
[5]
CHARACTERIZATION.
PubMed=7520570; DOI=10.1093/nar/22.15.3187;
Strauss E.J., Guthrie C.;
"PRP28, a 'DEAD-box' protein, is required for the first step of mRNA
splicing in vitro.";
Nucleic Acids Res. 22:3187-3193(1994).
[6]
MUTAGENESIS OF ALA-221; THR-223; ARG-264; GLU-265; THR-317; GLY-319;
MET-376; ALA-379; PRO-438; ILE-440; PHE-442; ALA-449; HIS-468;
ASN-486; MET-491; ARG-499; ASP-502; TYR-521; ARG-527; VAL-541;
ASP-546; LEU-549; LYS-580; ASN-584 AND ILE-586.
PubMed=9396812; DOI=10.1093/nar/25.24.5033;
Chang T.-H., Latus L.J., Liu Z., Abbott J.M.;
"Genetic interactions of conserved regions in the DEAD-box protein
Prp28p.";
Nucleic Acids Res. 25:5033-5040(1997).
[7]
FUNCTION.
PubMed=10024879; DOI=10.1016/S1097-2765(00)80174-4;
Staley J.P., Guthrie C.;
"An RNA switch at the 5' splice site requires ATP and the DEAD box
protein Prp28p.";
Mol. Cell 3:55-64(1999).
[8]
FUNCTION.
PubMed=11172727; DOI=10.1016/S1097-2765(01)00170-8;
Chen J.Y.-F., Stands L., Staley J.P., Jackups R.R. Jr., Latus L.J.,
Chang T.-H.;
"Specific alterations of U1-C protein or U1 small nuclear RNA can
eliminate the requirement of Prp28p, an essential DEAD box splicing
factor.";
Mol. Cell 7:227-232(2001).
[9]
IDENTIFICATION IN THE U5 SNRNP COMPLEX, AND IDENTIFICATION BY MASS
SPECTROMETRY.
PubMed=11720284;
Stevens S.W., Barta I., Ge H.Y., Moore R.E., Young M.K., Lee T.D.,
Abelson J.;
"Biochemical and genetic analyses of the U5, U6, and U4/U6 x U5 small
nuclear ribonucleoproteins from Saccharomyces cerevisiae.";
RNA 7:1543-1553(2001).
[10]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-69, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
-!- FUNCTION: ATP-dependent RNA helicase involved in mRNA splicing.
May destabilize the U1/5'-splice site duplex to permit an
effective competition for the 5'-splice site by the U6 snRNA,
resulting in the switch between U1 and U6 at the 5'-splice site.
May also act to unwind the U4/U6 base-pairing interaction in the
U4/U6/U5 snRNP, facilitating the first covalent step of splicing.
{ECO:0000269|PubMed:10024879, ECO:0000269|PubMed:11172727,
ECO:0000269|PubMed:2010088}.
-!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
-!- SUBUNIT: Component of the U5 snRNP complex, composed of at least
BRR2, PRP8, PRP28, DIB1, LIN1, SMB1, SMD1, SMD2, SMD3, SME1, SMX2,
SMX3, and SNU114, associated with the U5 snRNA.
{ECO:0000269|PubMed:11720284}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
Nucleus {ECO:0000269|PubMed:14562095}.
-!- DOMAIN: The Q motif is unique to and characteristic of the DEAD
box family of RNA helicases and controls ATP binding and
hydrolysis.
-!- SIMILARITY: Belongs to the DEAD box helicase family. DDX23/PRP28
subfamily. {ECO:0000305}.
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EMBL; X56934; CAA40255.1; -; Genomic_DNA.
EMBL; Z49701; CAA89729.1; -; Genomic_DNA.
EMBL; BK006938; DAA12083.1; -; Genomic_DNA.
PIR; A39624; A39624.
RefSeq; NP_010529.3; NM_001180551.3.
PDB; 4W7S; X-ray; 2.54 A; A/B=127-588.
PDBsum; 4W7S; -.
ProteinModelPortal; P23394; -.
SMR; P23394; -.
BioGrid; 32294; 240.
DIP; DIP-6324N; -.
IntAct; P23394; 19.
MINT; P23394; -.
STRING; 4932.YDR243C; -.
iPTMnet; P23394; -.
MaxQB; P23394; -.
PaxDb; P23394; -.
PRIDE; P23394; -.
EnsemblFungi; YDR243C; YDR243C; YDR243C.
GeneID; 851830; -.
KEGG; sce:YDR243C; -.
EuPathDB; FungiDB:YDR243C; -.
SGD; S000002651; PRP28.
GeneTree; ENSGT00880000138046; -.
HOGENOM; HOG000268796; -.
InParanoid; P23394; -.
KO; K12858; -.
OMA; NENDWRI; -.
OrthoDB; EOG092C1KT9; -.
BioCyc; YEAST:G3O-29816-MONOMER; -.
Reactome; R-SCE-72165; mRNA Splicing - Minor Pathway.
PRO; PR:P23394; -.
Proteomes; UP000002311; Chromosome IV.
GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
GO; GO:0005730; C:nucleolus; IBA:GO_Central.
GO; GO:0005682; C:U5 snRNP; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004004; F:ATP-dependent RNA helicase activity; ISS:SGD.
GO; GO:0000384; F:first spliceosomal transesterification activity; IMP:SGD.
GO; GO:0003723; F:RNA binding; IDA:SGD.
GO; GO:0000395; P:mRNA 5'-splice site recognition; IMP:SGD.
GO; GO:0010501; P:RNA secondary structure unwinding; IBA:GO_Central.
CDD; cd00079; HELICc; 1.
InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
InterPro; IPR014001; Helicase_ATP-bd.
InterPro; IPR001650; Helicase_C.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
Pfam; PF00270; DEAD; 1.
Pfam; PF00271; Helicase_C; 1.
SMART; SM00487; DEXDc; 1.
SMART; SM00490; HELICc; 1.
SUPFAM; SSF52540; SSF52540; 1.
PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
PROSITE; PS51194; HELICASE_CTER; 1.
PROSITE; PS51195; Q_MOTIF; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; Cytoplasm; Helicase;
Hydrolase; mRNA processing; mRNA splicing; Nucleotide-binding;
Nucleus; Phosphoprotein; Reference proteome.
CHAIN 1 588 Pre-mRNA-splicing ATP-dependent RNA
helicase PRP28.
/FTId=PRO_0000055127.
DOMAIN 208 399 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
DOMAIN 427 579 Helicase C-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00542}.
NP_BIND 221 228 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
MOTIF 172 202 Q motif.
MOTIF 341 344 DEAD box.
MOD_RES 69 69 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MUTAGEN 221 221 A->V: In PRP28-103; no growth at 15 and
37 degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 223 223 T->I: In PRP28-117; no growth at 15
degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 264 264 R->D,E: Lethal.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 265 265 E->Q: In PRP28-99; no growth at 15 and 37
degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 297 297 G->E: In PRP28-1; no growth at 15 degrees
Celsius. {ECO:0000269|PubMed:2010088}.
MUTAGEN 317 317 T->I: In PRP28-36; slow growth at 30
degrees Celsius, and no growth at 15 and
37 degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 317 317 T->Y: Lethal.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 319 319 G->E,V: No growth at 15 and 37 degrees
Celsius. {ECO:0000269|PubMed:9396812}.
MUTAGEN 376 376 M->I: In PRP28-32; no growth at 15
degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 379 379 A->W: In PRP28-102; no growth at 25
degrees Celsius or lower.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 438 438 P->L: In PRP28-61; no growth at 37
degrees Celsius; when associated with L-
468 and D-486.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 440 440 I->F: In PRP28-56; no growth at 37
degrees Celsius; when associated with S-
546 and E-584.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 442 442 F->G: In PRP28-101; no growth at 15 and
37 degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 442 442 F->S: In PRP28-55; no growth at 37
degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 449 449 A->T: In PRP28-66; no growth at 37
degrees Celsius; when associated with A-
541; V-549; N-580 and V-586.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 468 468 H->L: In PRP28-61; no growth at 37
degrees Celsius; when associated with L-
438 and D-486.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 486 486 N->D: In PRP28-61; no growth at 37
degrees Celsius; when associated with L-
438 and L-468.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 491 491 M->K: In PRP28-52; no growth at 37
degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 499 499 R->G: In PRP28-86; lethal.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 499 499 R->K: No growth at 15 degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 502 502 D->N: Lethal.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 521 521 Y->D: In PRP28-37; no growth at 37
degrees Celsius.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 527 527 R->D: Lethal.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 541 541 V->A: In PRP28-66; no growth at 37
degrees Celsius; when associated with T-
449; V-549; N-580 and V-586.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 546 546 D->S: In PRP28-56; no growth at 37
degrees Celsius; when associated with F-
440 and E-584.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 549 549 L->V: In PRP28-66; no growth at 37
degrees Celsius; when associated with T-
449; A-541; N-580 and V-586.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 580 580 K->N: In PRP28-66; no growth at 37
degrees Celsius; when associated with T-
449; A-541; V-549 and V-586.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 584 584 N->E: In PRP28-56; no growth at 37
degrees Celsius; when associated with F-
440 and S-546.
{ECO:0000269|PubMed:9396812}.
MUTAGEN 586 586 I->V: In PRP28-66; no growth at 37
degrees Celsius; when associated with T-
449; A-541; V-549 and N-580.
{ECO:0000269|PubMed:9396812}.
CONFLICT 493 493 A -> R (in Ref. 4; no nucleotide entry).
{ECO:0000305}.
HELIX 138 140 {ECO:0000244|PDB:4W7S}.
HELIX 143 145 {ECO:0000244|PDB:4W7S}.
HELIX 148 157 {ECO:0000244|PDB:4W7S}.
STRAND 160 166 {ECO:0000244|PDB:4W7S}.
STRAND 172 175 {ECO:0000244|PDB:4W7S}.
HELIX 182 190 {ECO:0000244|PDB:4W7S}.
HELIX 199 208 {ECO:0000244|PDB:4W7S}.
STRAND 217 220 {ECO:0000244|PDB:4W7S}.
HELIX 227 240 {ECO:0000244|PDB:4W7S}.
HELIX 247 253 {ECO:0000244|PDB:4W7S}.
STRAND 256 260 {ECO:0000244|PDB:4W7S}.
HELIX 264 283 {ECO:0000244|PDB:4W7S}.
STRAND 284 286 {ECO:0000244|PDB:4W7S}.
STRAND 291 294 {ECO:0000244|PDB:4W7S}.
HELIX 300 307 {ECO:0000244|PDB:4W7S}.
STRAND 312 316 {ECO:0000244|PDB:4W7S}.
HELIX 318 326 {ECO:0000244|PDB:4W7S}.
STRAND 337 340 {ECO:0000244|PDB:4W7S}.
HELIX 343 348 {ECO:0000244|PDB:4W7S}.
HELIX 352 365 {ECO:0000244|PDB:4W7S}.
STRAND 373 380 {ECO:0000244|PDB:4W7S}.
HELIX 383 392 {ECO:0000244|PDB:4W7S}.
STRAND 397 403 {ECO:0000244|PDB:4W7S}.
STRAND 410 417 {ECO:0000244|PDB:4W7S}.
HELIX 421 432 {ECO:0000244|PDB:4W7S}.
STRAND 439 442 {ECO:0000244|PDB:4W7S}.
HELIX 446 459 {ECO:0000244|PDB:4W7S}.
STRAND 464 467 {ECO:0000244|PDB:4W7S}.
HELIX 473 484 {ECO:0000244|PDB:4W7S}.
STRAND 487 493 {ECO:0000244|PDB:4W7S}.
TURN 495 500 {ECO:0000244|PDB:4W7S}.
STRAND 506 513 {ECO:0000244|PDB:4W7S}.
HELIX 518 525 {ECO:0000244|PDB:4W7S}.
STRAND 534 541 {ECO:0000244|PDB:4W7S}.
HELIX 547 559 {ECO:0000244|PDB:4W7S}.
HELIX 570 576 {ECO:0000244|PDB:4W7S}.
SEQUENCE 588 AA; 66641 MW; 333ADBF9D7C75C99 CRC64;
MARPIDVSQL IAGINKKKGL DENTSGKISK PRFLNKQERS KQERLKENEE SLTPTQSDSA
KVEIKKVNSR DDSFFNETND KKRNPSKQNG SKFHFSWNES EDTLSGYDPI VSTRAIDLLW
KGKTPKNAAE SSYMGKHWTE KSLHEMNERD WRILKEDYAI VTKGGTVENP LRNWEELNII
PRDLLRVIIQ ELRFPSPTPI QRITIPNVCN MKQYRDFLGV ASTGSGKTLA FVIPILIKMS
RSPPRPPSLK IIDGPKALIL APTRELVQQI QKETQKVTKI WSKESNYDCK VISIVGGHSL
EEISFSLSEG CDILVATPGR LIDSLENHLL VMKQVETLVL DEADKMIDLG FEDQVTNILT
KVDINADSAV NRQTLMFTAT MTPVIEKIAA GYMQKPVYAT IGVETGSEPL IQQVVEYADN
DEDKFKKLKP IVAKYDPPII IFINYKQTAD WLAEKFQKET NMKVTILHGS KSQEQREHSL
QLFRTNKVQI MIATNVAARG LDIPNVSLVV NFQISKKMDD YIHRIGRTGR AANEGTAVSF
VSAAEDESLI RELYKYVRKH DPLNSNIFSE AVKNKYNVGK QLSNEIIY


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G5488 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 (DHX16), Human, ELISA Kit 96T


 

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