P21372
Gene name |
PRP5 (RNA5, YBR237W, YBR1603) |
Protein name |
Pre-mRNA-processing ATP-dependent RNA helicase PRP5 |
Names |
|
Species |
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
KEGG Pathway |
sce:YBR237W |
EC number |
3.6.4.13: Acting on ATP; involved in cellular and subcellular movement |
Protein Class |
RNA HELICASE (PTHR24031) |
Descriptions
The DEAD-box adenosine triphosphatase (ATPase) Prp5p facilitates U2 small nuclear ribonucleoprotein particle (snRNP) binding to the intron branch site region during spliceosome assembly. Motifs in the DEAD box helicase domain are involved in ATP binding and ATP hydrolysis, whereas motifs in C-terminal helicase domain, potentially responsible for RNA-binding or ATP coordination.
There is a unique interdomain interaction between the DEAD box helicase domain and helicase domain in which the C-terminal helicase domain clashes with the RNA-binding surface. Destabilizing this interaction accelerates RNA duplex unwinding, suggesting that it is present in solution and inhibitory for catalysis. The N-terminal flanking sequence to the DEAD box helicase interacts with DEAD box helicase domain and C-terminal helicase domain, specifically the linker region between the two domains, and stabilizes the autoinhibited state.
Autoinhibitory domains (AIDs)
Target domain |
480-629 (C-terminal helicase domain) |
Relief mechanism |
|
Assay |
Structural analysis |
Target domain |
256-470 (DEAD box helicase domain) |
Relief mechanism |
|
Assay |
Structural analysis, Mutagenesis experiment |
Target domain |
256-470 (DEAD box helicase domain); 480-629 (C-terminal helicase domain) |
Relief mechanism |
|
Assay |
Structural analysis |
Accessory elements
No accessory elements
References
- Floor SN et al. (2016) "Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3", The Journal of biological chemistry, 291, 2412-21
- Zhang ZM et al. (2013) "Crystal structure of Prp5p reveals interdomain interactions that impact spliceosome assembly", Cell reports, 5, 1269-78
Autoinhibited structure
Activated structure
5 structures for P21372
| Entry ID | Method | Resolution | Chain | Position | Source |
|---|---|---|---|---|---|
| 4LJY | X-ray | 195 A | A | 206-698 | PDB |
| 4LK2 | X-ray | 212 A | A/B | 206-698 | PDB |
| 7OQB | EM | 900 A | p | 1-849 | PDB |
| 7OQE | EM | 590 A | p | 1-849 | PDB |
| AF-P21372-F1 | Predicted | AlphaFoldDB |
21 variants for P21372
| Variant ID(s) | Position | Change | Description | Diseaes Association | Provenance |
|---|---|---|---|---|---|
| s02-692078 | 39 | H>N | No | SGRP | |
| s02-692121 | 53 | G>A | No | SGRP | |
| s02-692190 | 76 | N>S | No | SGRP | |
| s02-692346 | 128 | A>V | No | SGRP | |
| s02-692361 | 133 | N>I | No | SGRP | |
| s02-692614 | 217 | N>K | No | SGRP | |
| s02-692675 | 238 | L>F | No | SGRP | |
| s02-693264 | 434 | K>R | No | SGRP | |
| s02-693386 | 475 | V>I | No | SGRP | |
| s02-693464 | 501 | H>D | No | SGRP | |
| s02-693464 | 501 | H>Y | No | SGRP | |
| s02-693902 | 647 | E>K | No | SGRP | |
| s02-693918 | 652 | L>S | No | SGRP | |
| s02-693920 | 653 | D>N | No | SGRP | |
| s02-693923 | 654 | P>S | No | SGRP | |
| s02-694119 | 719 | S>N | No | SGRP | |
| s02-694128 | 722 | R>H | No | SGRP | |
| s02-694146 | 728 | V>E | No | SGRP | |
| s02-694148 | 729 | S>P | No | SGRP | |
| s02-694155 | 731 | S>F | No | SGRP | |
| s02-694469 | 836 | V>I | No | SGRP |
No associated diseases with P21372
No regional properties for P21372
| Type | Name | Position | InterPro Accession |
|---|---|---|---|
| No domain, repeats, and functional sites for P21372 | |||
Functions
| Description | ||
|---|---|---|
| EC Number | 3.6.4.13 | Acting on ATP; involved in cellular and subcellular movement |
| Subcellular Localization |
|
|
| PANTHER Family | PTHR24031 | RNA HELICASE |
| PANTHER Subfamily | PTHR24031:SF25 | ATP-DEPENDENT RNA HELICASE DDX46-RELATED |
| PANTHER Protein Class | RNA helicase | |
| PANTHER Pathway Category | No pathway information available | |
2 GO annotations of cellular component
| Name | Definition |
|---|---|
| commitment complex | A spliceosomal complex that is formed by association of the U1 snRNP with the 5' splice site of an unspliced intron in an RNA transcript. |
| nucleus | A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. |
5 GO annotations of molecular function
| Name | Definition |
|---|---|
| ATP binding | Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. |
| ATP hydrolysis activity | Catalysis of the reaction |
| ATP-dependent activity, acting on RNA | Catalysis of the reaction |
| nucleic acid binding | Binding to a nucleic acid. |
| RNA helicase activity | Unwinding of an RNA helix, driven by ATP hydrolysis. |
2 GO annotations of biological process
| Name | Definition |
|---|---|
| mRNA branch site recognition | Recognition of the pre-mRNA branch site sequence by components of the assembling spliceosome. |
| mRNA splicing, via spliceosome | The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced. |
12 homologous proteins in AiPD
| UniProt AC | Gene Name | Protein Name | Species | Evidence Code |
|---|---|---|---|---|
| P10081 | TIF2 | ATP-dependent RNA helicase eIF4A | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PR |
| P15424 | MSS116 | ATP-dependent RNA helicase MSS116, mitochondrial | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PR |
| P53166 | MRH4 | ATP-dependent RNA helicase MRH4, mitochondrial | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PR |
| Q03532 | HAS1 | ATP-dependent RNA helicase HAS1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PR |
| Q06218 | DBP9 | ATP-dependent RNA helicase DBP9 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PR |
| P20448 | HCA4 | ATP-dependent RNA helicase HCA4 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PR |
| P32892 | DRS1 | ATP-dependent RNA helicase DRS1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PR |
| P45818 | ROK1 | ATP-dependent RNA helicase ROK1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PR |
| Q7L014 | DDX46 | Probable ATP-dependent RNA helicase DDX46 | Homo sapiens (Human) | PR |
| Q569Z5 | Ddx46 | Probable ATP-dependent RNA helicase DDX46 | Mus musculus (Mouse) | PR |
| Q62780 | Ddx46 | Probable ATP-dependent RNA helicase DDX46 | Rattus norvegicus (Rat) | PR |
| Q8H0U8 | RH42 | DEAD-box ATP-dependent RNA helicase 42 | Arabidopsis thaliana (Mouse-ear cress) | SS |
| 10 | 20 | 30 | 40 | 50 | 60 |
| METIDSKQNI | NRESLLEERR | KKLAKWKQKK | AQFDAQKEHQ | TSRNDIVTNS | LEGKQTTEKF |
| 70 | 80 | 90 | 100 | 110 | 120 |
| TERQERVKEE | LRKRKNEFRK | SDEPVSVKPS | KKKSKRSKVK | KKISFDFSDD | DDSEIGVSFR |
| 130 | 140 | 150 | 160 | 170 | 180 |
| SKEHIQKAPE | HDNEKDPLDE | FMTSLKEEKM | SNSKGMYDRG | DILDVEDQLF | ELGGTDDEDV |
| 190 | 200 | 210 | 220 | 230 | 240 |
| EDNTDNSNIA | KIAKLKAKKR | VKQIYYSPEE | LEPFQKNFYI | ESETVSSMSE | MEVEELRLSL |
| 250 | 260 | 270 | 280 | 290 | 300 |
| DNIKIKGTGC | PKPVTKWSQL | GLSTDTMVLI | TEKLHFGSLT | PIQSQALPAI | MSGRDVIGIS |
| 310 | 320 | 330 | 340 | 350 | 360 |
| KTGSGKTISY | LLPLLRQVKA | QRPLSKHETG | PMGLILAPTR | ELALQIHEEV | TKFTEADTSI |
| 370 | 380 | 390 | 400 | 410 | 420 |
| RSVCCTGGSE | MKKQITDLKR | GTEIVVATPG | RFIDILTLND | GKLLSTKRIT | FVVMDEADRL |
| 430 | 440 | 450 | 460 | 470 | 480 |
| FDLGFEPQIT | QIMKTVRPDK | QCVLFSATFP | NKLRSFAVRV | LHSPISITIN | SKGMVNENVK |
| 490 | 500 | 510 | 520 | 530 | 540 |
| QKFRICHSED | EKFDNLVQLI | HERSEFFDEV | QSENDGQSSD | VEEVDAKAII | FVSSQNICDF |
| 550 | 560 | 570 | 580 | 590 | 600 |
| ISKKLLNAGI | VTCAIHAGKP | YQERLMNLEK | FKREKNSILL | CTEVLSRGLN | VPEVSLVIIY |
| 610 | 620 | 630 | 640 | 650 | 660 |
| NAVKTFAQYV | HTTGRTARGS | RSGTAITLLL | HDELSGAYIL | SKAMRDEEIK | ALDPLQAKEL |
| 670 | 680 | 690 | 700 | 710 | 720 |
| QEMSAKFESG | MKKGKFRLSK | GFGGKGLENI | KSKREEAQNK | DLELKKNDKR | SDDLEKKISN |
| 730 | 740 | 750 | 760 | 770 | 780 |
| PREGHDSVSE | SSALIPRLNY | ELFKESTDGS | IIFYAKVYIN | DLPQIVRWEA | TKNTTLLFIK |
| 790 | 800 | 810 | 820 | 830 | 840 |
| HETGCSITNK | GKFYPEGKEP | KNENDEPKLY | LLIEGQDEKD | IQLSIELLEQ | KVKEGVVKAA |
| SLSLKSTKY |