PDBsum entry 1s2m

RNA binding protein

PDB id

1s2m

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Contents

			Protein chain

					377 a.a. *

			Waters ×253

* Residue conservation analysis

PDB id:

1s2m

Links

Name:

RNA binding protein

Title:

Crystal structure of the dead box protein dhh1p

Structure:

Putative atp-dependent RNA helicase dhh1. Chain: a. Fragment: core RNA helicase fragment. Synonym: dead box RNA helicase dhh1p. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: dhh1, ydl160c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å

R-factor:

0.202

R-free:

0.234

Authors:

Z.Cheng,H.Song

Key ref:

Z.Cheng et al. (2005). Crystal structure and functional analysis of DEAD-box protein Dhh1p. Rna, 11, 1258-1270. PubMed id: 15987810

Date:

09-Jan-04

Release date:

01-Mar-05

PROCHECK

	Headers

	References

Protein chain

P39517 (DHH1_YEAST) - ATP-dependent RNA helicase DHH1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: Struc:					506 a.a. 377 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	+	phosphate	+	H(+)

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

reference

	Rna 11:1258-1270 (2005)
PubMed id: 15987810

Crystal structure and functional analysis of DEAD-box protein Dhh1p.
Z.Cheng, J.Coller, R.Parker, H.Song.

ABSTRACT

The control of mRNA translation and degradation are critical for proper gene expression. A key regulator of both translation and degradation is Dhh1p, which is a DEAD-box protein, and functions both to repress translation and enhance decapping. We describe the crystal structure of the N- and C-terminal truncated Dhh1p (tDhh1p) determined at 2.1 A resolution. This reveals that, like other DEAD-box proteins, tDhh1p contains two RecA-like domains, although with a unique arrangement. In contrast to eIF4A and mjDEAD, in which no motif interactions exist, in Dhh1p, motif V interacts with motif I and the Q-motif, thereby linking the two domains together. Electrostatic potential mapping combined with mutagenesis reveals that motifs I, V, and VI are involved in RNA binding. In addition, trypsin digestion of tDhh1p suggests that ATP binding enhances an RNA-induced conformational change. Interestingly, some mutations located in the conserved motifs and at the interface between the two Dhh1 domains confer dominant negative phenotypes in vivo and disrupt the conformational switch in vitro. This suggests that this conformational change is required in Dhh1 function and identifies key residues involved in that transition.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20339440

E.R.Yassin, A.M.Abdul-Nabi, A.Takeda, and N.R.Yaseen (2010).
Effects of the NUP98-DDX10 oncogene on primary human CD34+ cells: role of a conserved helicase motif.

Leukemia, 24, 1001-1011.

20071466

L.Tang, T.Machacek, Y.M.Mamnun, A.Penkner, J.Gloggnitzer, C.Wegrostek, R.Konrat, M.F.Jantsch, J.Loidl, and V.Jantsch (2010).
Mutations in Caenorhabditis elegans him-19 show meiotic defects that worsen with age.

Mol Biol Cell, 21, 885-896.

20471947

R.Perriman, and M.Ares (2010).
Invariant U2 snRNA nucleotides form a stem loop to recognize the intron early in splicing.

Mol Cell, 38, 416-427.

20124414

S.Kramer, R.Queiroz, L.Ellis, J.D.Hoheisel, C.Clayton, and M.Carrington (2010).
The RNA helicase DHH1 is central to the correct expression of many developmentally regulated mRNAs in trypanosomes.

J Cell Sci, 123, 699-711.

20832728

T.Nissan, P.Rajyaguru, M.She, H.Song, and R.Parker (2010).
Decapping activators in Saccharomyces cerevisiae act by multiple mechanisms.

Mol Cell, 39, 773-783.

19361491

A.Hubert, and P.Anderson (2009).
The C. elegans sex determination gene laf-1 encodes a putative DEAD-box RNA helicase.

Dev Biol, 330, 358-367.

19474341

A.R.Karow, and D.Klostermeier (2009).
A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN.

Nucleic Acids Res, 37, 4464-4471.

19050012

D.Klostermeier, and M.G.Rudolph (2009).
A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility.

Nucleic Acids Res, 37, 421-430.

PDB codes:

3eaq 3ear 3eas

19285948

F.Tritschler, J.E.Braun, A.Eulalio, V.Truffault, E.Izaurralde, and O.Weichenrieder (2009).
Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B.

Mol Cell, 33, 661-668.

PDB codes:

2wax 2way

19219046

H.von Moeller, C.Basquin, and E.Conti (2009).
The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner.

Nat Struct Mol Biol, 16, 247-254.

PDB codes:

3fhc 3fht

19317511

K.M.Sinha, M.S.Glickman, and S.Shuman (2009).
Mutational analysis of Mycobacterium UvrD1 identifies functional groups required for ATP hydrolysis, DNA unwinding, and chemomechanical coupling.

Biochemistry, 48, 4019-4030.

19710183

M.G.Rudolph, and D.Klostermeier (2009).
The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core.

RNA, 15, 1993-2001.

PDB codes:

3i31 3i32

19747077

M.Hilbert, A.R.Karow, and D.Klostermeier (2009).
The mechanism of ATP-dependent RNA unwinding by DEAD box proteins.

Biol Chem, 390, 1237-1250.

19297524

N.Minshall, M.Kress, D.Weil, and N.Standart (2009).
Role of p54 RNA helicase activity and its C-terminal domain in translational repression, P-body localization and assembly.

Mol Biol Cell, 20, 2464-2472.

19589129

S.H.Ling, Z.Cheng, and H.Song (2009).
Structural aspects of RNA helicases in eukaryotic mRNA decay.

Biosci Rep, 29, 339-349.

19015546

V.Balagopal, and R.Parker (2009).
Stm1 Modulates mRNA Decay and Dhh1 Function in Saccharomyces cerevisiae.

Genetics, 181, 93.

19805289

Z.Y.Dossani, C.S.Weirich, J.P.Erzberger, J.M.Berger, and K.Weis (2009).
Structure of the C-terminus of the mRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1.

Proc Natl Acad Sci U S A, 106, 16251-16256.

PDB code:

3gfp

18184816

B.Theissen, A.R.Karow, J.Köhler, A.Gubaev, and D.Klostermeier (2008).
Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase.

Proc Natl Acad Sci U S A, 105, 548-553.

18715869

E.Pedro-Segura, S.V.Vergara, S.Rodríguez-Navarro, R.Parker, D.J.Thiele, and S.Puig (2008).
The Cth2 ARE-binding protein recruits the Dhh1 helicase to promote the decay of succinate dehydrogenase SDH4 mRNA in response to iron deficiency.

J Biol Chem, 283, 28527-28535.

18765641

F.Tritschler, A.Eulalio, S.Helms, S.Schmidt, M.Coles, O.Weichenrieder, E.Izaurralde, and V.Truffault (2008).
Similar modes of interaction enable Trailer Hitch and EDC3 to associate with DCP1 and Me31B in distinct protein complexes.

Mol Cell Biol, 28, 6695-6708.

PDB codes:

2vxe 2vxf

18042682

X.Zhang, T.Nakashima, Y.Kakuta, M.Yao, I.Tanaka, and M.Kimura (2008).
Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.

Protein Sci, 17, 136-145.

PDB code:

2z41

17229151

A.R.Karow, B.Theissen, and D.Klostermeier (2007).
Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains.

FEBS J, 274, 463-473.

17984320

C.J.Decker, D.Teixeira, and R.Parker (2007).
Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae.

J Cell Biol, 179, 437-449.

17574830

E.Jankowsky, and M.E.Fairman (2007).
RNA helicases--one fold for many functions.

Curr Opin Struct Biol, 17, 316-324.

17923697

F.Tritschler, A.Eulalio, V.Truffault, M.D.Hartmann, S.Helms, S.Schmidt, M.Coles, E.Izaurralde, and O.Weichenrieder (2007).
A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting.

Mol Cell Biol, 27, 8600-8611.

PDB codes:

2rm4 2vc8

16769775

A.Weston, and J.Sommerville (2006).
Xp54 and related (DDX6-like) RNA helicases: roles in messenger RNP assembly, translation regulation and RNA degradation.

Nucleic Acids Res, 34, 3082-3094.

17142894

J.M.Caruthers, Y.Hu, and D.B.McKay (2006).
Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1191-1195.

PDB code:

2hjv

16532013

M.E.Bordeleau, A.Mori, M.Oberer, L.Lindqvist, L.S.Chard, T.Higa, G.J.Belsham, G.Wagner, J.Tanaka, and J.Pelletier (2006).
Functional characterization of IRESes by an inhibitor of the RNA helicase eIF4A.

Nat Chem Biol, 2, 213-220.

16687655

R.Dhalia, N.Marinsek, C.R.Reis, R.Katz, J.R.Muniz, N.Standart, M.Carrington, and O.P.de Melo Neto (2006).
The two eIF4A helicases in Trypanosoma brucei are functionally distinct.

Nucleic Acids Res, 34, 2495-2507.

16611943

S.Wang, Y.Hu, M.T.Overgaard, F.V.Karginov, O.C.Uhlenbeck, and D.B.McKay (2006).
The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold.

RNA, 12, 959-967.

PDB code:

2g0c

16630817

T.Sengoku, O.Nureki, A.Nakamura, S.Kobayashi, and S.Yokoyama (2006).
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.

Cell, 125, 287-300.

PDB code:

2db3

16179257

J.Coller, and R.Parker (2005).
General translational repression by activators of mRNA decapping.

Cell, 122, 875-886.

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 codes are shown on the right.