7pmq: Difference between revisions

Latest revision as of 19:12, 8 September 2026

DEAD-box helicase DbpA in the active conformation bound to a hairpin loop RNA and ADP/BeF3

Structural highlights

7pmq is a 8 chain structure with sequence from Escherichia coli and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.22Å
Ligands:	ADP, BEF, MG, PO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DBPA_ECOLI DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes. Requires a single-stranded RNA loading site on the 3' side of the substrate helix.[HAMAP-Rule:MF_00965]^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

References

↑ Tsu CA, Kossen K, Uhlenbeck OC. The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA. 2001 May;7(5):702-9. doi: 10.1017/s1355838201010135. PMID:11350034 doi:https://dx.doi.org/10.1017/s1355838201010135
↑ Diges CM, Uhlenbeck OC. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J. 2001 Oct 1;20(19):5503-12. doi: 10.1093/emboj/20.19.5503. PMID:11574482 doi:https://dx.doi.org/10.1093/emboj/20.19.5503
↑ Diges CM, Uhlenbeck OC. Escherichia coli DbpA is a 3' --> 5' RNA helicase. Biochemistry. 2005 May 31;44(21):7903-11. doi: 10.1021/bi050033x. PMID:15910005 doi:https://dx.doi.org/10.1021/bi050033x
↑ Henn A, Cao W, Hackney DD, De La Cruz EM. The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA. J Mol Biol. 2008 Mar 14;377(1):193-205. doi: 10.1016/j.jmb.2007.12.046. Epub 2007, Dec 28. PMID:18237742 doi:https://dx.doi.org/10.1016/j.jmb.2007.12.046
↑ Sharpe Elles LM, Sykes MT, Williamson JR, Uhlenbeck OC. A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic Acids Res. 2009 Oct;37(19):6503-14. doi: 10.1093/nar/gkp711. Epub 2009, Sep 4. PMID:19734347 doi:https://dx.doi.org/10.1093/nar/gkp711
↑ Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD, De La Cruz EM. Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA. Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4046-50. doi:, 10.1073/pnas.0913081107. Epub 2010 Feb 16. PMID:20160110 doi:https://dx.doi.org/10.1073/pnas.0913081107
↑ Fuller-Pace FV, Nicol SM, Reid AD, Lane DP. DbpA: a DEAD box protein specifically activated by 23s rRNA. EMBO J. 1993 Sep;12(9):3619-26. PMID:8253085
↑ Boddeker N, Stade K, Franceschi F. Characterization of DbpA, an Escherichia coli DEAD box protein with ATP independent RNA unwinding activity. Nucleic Acids Res. 1997 Feb 1;25(3):537-45. doi: 10.1093/nar/25.3.537. PMID:9016593 doi:https://dx.doi.org/10.1093/nar/25.3.537
↑ Tsu CA, Uhlenbeck OC. Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA. Biochemistry. 1998 Dec 1;37(48):16989-96. doi: 10.1021/bi981837y. PMID:9836593 doi:https://dx.doi.org/10.1021/bi981837y

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OCA

[1] Tsu CA, Kossen K, Uhlenbeck OC. The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA. 2001 May;7(5):702-9. doi: 10.1017/s1355838201010135. PMID:11350034 doi:https://dx.doi.org/10.1017/s1355838201010135

[2] Diges CM, Uhlenbeck OC. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J. 2001 Oct 1;20(19):5503-12. doi: 10.1093/emboj/20.19.5503. PMID:11574482 doi:https://dx.doi.org/10.1093/emboj/20.19.5503

[3] Diges CM, Uhlenbeck OC. Escherichia coli DbpA is a 3' --> 5' RNA helicase. Biochemistry. 2005 May 31;44(21):7903-11. doi: 10.1021/bi050033x. PMID:15910005 doi:https://dx.doi.org/10.1021/bi050033x

[4] Henn A, Cao W, Hackney DD, De La Cruz EM. The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA. J Mol Biol. 2008 Mar 14;377(1):193-205. doi: 10.1016/j.jmb.2007.12.046. Epub 2007, Dec 28. PMID:18237742 doi:https://dx.doi.org/10.1016/j.jmb.2007.12.046

[5] Sharpe Elles LM, Sykes MT, Williamson JR, Uhlenbeck OC. A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic Acids Res. 2009 Oct;37(19):6503-14. doi: 10.1093/nar/gkp711. Epub 2009, Sep 4. PMID:19734347 doi:https://dx.doi.org/10.1093/nar/gkp711

[6] Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD, De La Cruz EM. Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA. Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4046-50. doi:, 10.1073/pnas.0913081107. Epub 2010 Feb 16. PMID:20160110 doi:https://dx.doi.org/10.1073/pnas.0913081107

[7] Fuller-Pace FV, Nicol SM, Reid AD, Lane DP. DbpA: a DEAD box protein specifically activated by 23s rRNA. EMBO J. 1993 Sep;12(9):3619-26. PMID:8253085

[8] Boddeker N, Stade K, Franceschi F. Characterization of DbpA, an Escherichia coli DEAD box protein with ATP independent RNA unwinding activity. Nucleic Acids Res. 1997 Feb 1;25(3):537-45. doi: 10.1093/nar/25.3.537. PMID:9016593 doi:https://dx.doi.org/10.1093/nar/25.3.537

[9] Tsu CA, Uhlenbeck OC. Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA. Biochemistry. 1998 Dec 1;37(48):16989-96. doi: 10.1021/bi981837y. PMID:9836593 doi:https://dx.doi.org/10.1021/bi981837y

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7pmq is ON HOLD
+==DEAD-box helicase DbpA in the active conformation bound to a hairpin loop RNA and ADP/BeF3==
+<StructureSection load='7pmq' size='340' side='right'caption='[[7pmq]], [[Resolution|resolution]] 3.22&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7pmq]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PMQ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.22&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=7pmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pmq OCA], [https://pdbe.org/7pmq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pmq RCSB], [https://www.ebi.ac.uk/pdbsum/7pmq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pmq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DBPA_ECOLI DBPA_ECOLI] DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes. Requires a single-stranded RNA loading site on the 3' side of the substrate helix.[HAMAP-Rule:MF_00965]<ref>PMID:11350034</ref> <ref>PMID:11574482</ref> <ref>PMID:15910005</ref> <ref>PMID:18237742</ref> <ref>PMID:19734347</ref> <ref>PMID:20160110</ref> <ref>PMID:8253085</ref> <ref>PMID:9016593</ref> <ref>PMID:9836593</ref>
-Authors:
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
-Description:
+== References ==
-[[Category: Unreleased Structures]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Wurm JP]]

7pmq: Difference between revisions

Latest revision as of 19:12, 8 September 2026

DEAD-box helicase DbpA in the active conformation bound to a hairpin loop RNA and ADP/BeF3

Structural highlights

Function

See Also

References

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