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 9: / Line 9: @@
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/W8TF60_ECOLX W8TF60_ECOLX] 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.[HAMAP-Rule:MF_00965]
+[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>
 ==See Also==
 *[[Helicase 3D structures|Helicase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>

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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