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4xw3

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Crystal structure of the SPRY domain of the human DEAD-box protein DDX1

Structural highlights

4xw3 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DDX1_HUMAN Acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the NF-kappa-B promoter region via association with RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. Component of the tRNA-splicing ligase complex required to facilitate the enzymatic turnover of catalytic subunit RTCB: together with archease (ZBTB8OS), acts by facilitating the guanylylation of RTCB, a key intermediate step in tRNA ligation (PubMed:24870230). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of pro-inflammatory cytokines via the adapter molecule TICAM1. Specifically binds (via helicase ATP-binding domain) on both short and long poly(I:C) dsRNA (By similarity).[UniProtKB:Q91VR5]^[1] ^[2] ^[3] ^[4] ^[5] ^[6] (Microbial infection) Required for HIV-1 Rev function as well as for HIV-1 and coronavirus IBV replication. Binds to the RRE sequence of HIV-1 mRNAs.^[7] (Microbial infection) Required for Coronavirus IBV replication.^[8]

Publication Abstract from PubMed

The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein-protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 A resolution. The structure reveals two layers of concave, antiparallel beta-sheets that stack onto each other and a third beta-sheet beneath the beta-sandwich. A comparison with SPRY-domain structures from other eukaryotic proteins showed that the general beta-sandwich fold is conserved; however, differences were detected in the loop regions, which were identified in other SPRY domains to be essential for interaction with cognate partners. In contrast, in hDSPRY these loop regions are not strictly conserved across species. Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein-protein interaction surface. The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein. By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein.,Kellner JN, Meinhart A Acta Crystallogr F Struct Biol Commun. 2015 Sep 1;71(Pt 9):1176-88. doi:, 10.1107/S2053230X15013709. Epub 2015 Aug 25. PMID:26323305^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Chen HC, Lin WC, Tsay YG, Lee SC, Chang CJ. An RNA helicase, DDX1, interacting with poly(A) RNA and heterogeneous nuclear ribonucleoprotein K. J Biol Chem. 2002 Oct 25;277(43):40403-9. PMID:12183465 doi:10.1074/jbc.M206981200
↑ Fang J, Kubota S, Yang B, Zhou N, Zhang H, Godbout R, Pomerantz RJ. A DEAD box protein facilitates HIV-1 replication as a cellular co-factor of Rev. Virology. 2004 Dec 20;330(2):471-80. PMID:15567440 doi:10.1016/j.virol.2004.09.039
↑ Onishi H, Kino Y, Morita T, Futai E, Sasagawa N, Ishiura S. MBNL1 associates with YB-1 in cytoplasmic stress granules. J Neurosci Res. 2008 Jul;86(9):1994-2002. doi: 10.1002/jnr.21655. PMID:18335541 doi:10.1002/jnr.21655
↑ Li L, Monckton EA, Godbout R. A role for DEAD box 1 at DNA double-strand breaks. Mol Cell Biol. 2008 Oct;28(20):6413-25. PMID:18710941 doi:10.1128/MCB.01053-08
↑ Xu L, Khadijah S, Fang S, Wang L, Tay FP, Liu DX. The cellular RNA helicase DDX1 interacts with coronavirus nonstructural protein 14 and enhances viral replication. J Virol. 2010 Sep;84(17):8571-83. PMID:20573827 doi:10.1128/JVI.00392-10
↑ Popow J, Jurkin J, Schleiffer A, Martinez J. Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors. Nature. 2014 Jul 3;511(7507):104-7. PMID:24870230 doi:10.1038/nature13284
↑ Fang J, Kubota S, Yang B, Zhou N, Zhang H, Godbout R, Pomerantz RJ. A DEAD box protein facilitates HIV-1 replication as a cellular co-factor of Rev. Virology. 2004 Dec 20;330(2):471-80. PMID:15567440 doi:10.1016/j.virol.2004.09.039
↑ Xu L, Khadijah S, Fang S, Wang L, Tay FP, Liu DX. The cellular RNA helicase DDX1 interacts with coronavirus nonstructural protein 14 and enhances viral replication. J Virol. 2010 Sep;84(17):8571-83. PMID:20573827 doi:10.1128/JVI.00392-10
↑ Kellner JN, Meinhart A. Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein. Acta Crystallogr F Struct Biol Commun. 2015 Sep 1;71(Pt 9):1176-88. doi:, 10.1107/S2053230X15013709. Epub 2015 Aug 25. PMID:26323305 doi:http://dx.doi.org/10.1107/S2053230X15013709

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4xw3"

Categories: Homo sapiens | Large Structures | Kellner JN | Meinhart A

@@ Line 1: / Line 1: @@
 ==Crystal structure of the SPRY domain of the human DEAD-box protein DDX1==
-<StructureSection load='4xw3' size='340' side='right' caption='[[4xw3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='4xw3' size='340' side='right'caption='[[4xw3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xw3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XW3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xw3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XW3 FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xw3 RCSB], [http://www.ebi.ac.uk/pdbsum/4xw3 PDBsum]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xw3 OCA], [https://pdbe.org/4xw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xw3 RCSB], [https://www.ebi.ac.uk/pdbsum/4xw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xw3 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DDX1_HUMAN DDX1_HUMAN] Acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the NF-kappa-B promoter region via association with RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. Component of the tRNA-splicing ligase complex required to facilitate the enzymatic turnover of catalytic subunit RTCB: together with archease (ZBTB8OS), acts by facilitating the guanylylation of RTCB, a key intermediate step in tRNA ligation (PubMed:24870230). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of pro-inflammatory cytokines via the adapter molecule TICAM1. Specifically binds (via helicase ATP-binding domain) on both short and long poly(I:C) dsRNA (By similarity).[UniProtKB:Q91VR5]<ref>PMID:12183465</ref> <ref>PMID:15567440</ref> <ref>PMID:18335541</ref> <ref>PMID:18710941</ref> <ref>PMID:20573827</ref> <ref>PMID:24870230</ref>   (Microbial infection) Required for HIV-1 Rev function as well as for HIV-1 and coronavirus IBV replication. Binds to the RRE sequence of HIV-1 mRNAs.<ref>PMID:15567440</ref>   (Microbial infection) Required for Coronavirus IBV replication.<ref>PMID:20573827</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 13: / Line 17: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4xw3" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Kellner, J N]]
+[[Category: Homo sapiens]]
-[[Category: Meinhart, A]]
+[[Category: Large Structures]]
-[[Category: Beta-sandwich]]
+[[Category: Kellner JN]]
-[[Category: Dead-box protein]]
+[[Category: Meinhart A]]
-[[Category: Hydrolase]]
-[[Category: Insertion domain]]
-[[Category: Spry domain]]

4xw3

From Proteopedia

Current revision

Crystal structure of the SPRY domain of the human DEAD-box protein DDX1

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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