PDBsum entry 3kx2

Hydrolase

PDB id

3kx2

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Contents

			Protein chains

					755 a.a. *

			Ligands

					ADP ×2

			Metals

					_MG ×2

			Waters ×982

* Residue conservation analysis

PDB id:

3kx2

Links

Name:

Hydrolase

Title:

Crystal structure of prp43p in complex with adp

Structure:

Pre-mRNA-splicing factor atp-dependent RNA helicase prp43. Chain: b, a. Synonym: prp43p, helicase ja1. Engineered: yes

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 559292. Strain: s288c. Gene: ygl120c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å

R-factor:

0.209

R-free:

0.250

Authors:

K.H.Nielsen,G.R.Andersen,Y.He

Key ref:

Y.He et al. (2010). Structural basis for the function of DEAH helicases. Embo Rep, 11, 180-186. PubMed id: 20168331

Date:

02-Dec-09

Release date:

26-Jan-10

PROCHECK

	Headers

	References

Protein chains

P53131 (PRP43_YEAST) - Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: Struc:

Seq: Struc:					767 a.a. 755 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.6.4.13 - Rna helicase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP

H2O

ADP
Bound ligand (Het Group name = ADP)
corresponds exactly

phosphate

H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

	Embo Rep 11:180-186 (2010)
PubMed id: 20168331

Structural basis for the function of DEAH helicases.
Y.He, G.R.Andersen, K.H.Nielsen.

ABSTRACT

DEAH helicases participate in pre-messenger RNA splicing and ribosome biogenesis. The structure of yeast Prp43p-ADP reveals the homology of DEAH helicases to DNA helicases and the presence of an oligonucleotide-binding motif. A beta-hairpin from the second RecA domain is wedged between two carboxy-terminal domains and blocks access to the occluded RNA binding site formed by the RecA domains and a C-terminal domain. ATP binding and hydrolysis are likely to induce conformational changes in the hairpin that are important for RNA unwinding or ribonucleoprotein remodelling. The structure of Prp43p provides the framework for functional and genetic analysis of all DEAH helicases.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20971974

B.Kolaczkowski, D.N.Hupalo, and A.D.Kern (2011).
Recurrent adaptation in RNA interference genes across the Drosophila phylogeny.

Mol Biol Evol, 28, 1033-1042.

20813532

E.Jankowsky (2011).
RNA helicases at work: binding and rearranging.

Trends Biochem Sci, 36, 19-29.

21265761

I.L.Woodman, and E.L.Bolt (2011).
Winged helix domains with unknown function in Hel308 and related helicases.

Biochem Soc Trans, 39, 140-144.

20566885

J.R.Weir, F.Bonneau, J.Hentschel, and E.Conti (2010).
Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance.

Proc Natl Acad Sci U S A, 107, 12139-12144.

PDB code:

2xgj

20941364

P.Schütz, T.Karlberg, S.van den Berg, R.Collins, L.Lehtiö, M.Högbom, L.Holmberg-Schiavone, W.Tempel, H.W.Park, M.Hammarström, M.Moche, A.G.Thorsell, and H.Schüler (2010).
Comparative structural analysis of human DEAD-box RNA helicases.

PLoS One, 5, 0.

PDB codes:

2g9n 2p6n 2pl3 2rb4 3b7g 3ber 3bor 3dkp 3fe2 3iuy 3ly5

20512111

R.N.Jackson, A.A.Klauer, B.J.Hintze, H.Robinson, A.van Hoof, and S.J.Johnson (2010).
The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing.

EMBO J, 29, 2205-2216.

PDB code:

3l9o

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.