1hq1: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:1hq1.png|left|200px]]


<!--
==STRUCTURAL AND ENERGETIC ANALYSIS OF RNA RECOGNITION BY A UNIVERSALLY CONSERVED PROTEIN FROM THE SIGNAL RECOGNITION PARTICLE==
The line below this paragraph, containing "STRUCTURE_1hq1", creates the "Structure Box" on the page.
<StructureSection load='1hq1' size='340' side='right'caption='[[1hq1]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1hq1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HQ1 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.52&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
{{STRUCTURE_1hq1|  PDB=1hq1  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1hq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hq1 OCA], [https://pdbe.org/1hq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hq1 RCSB], [https://www.ebi.ac.uk/pdbsum/1hq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hq1 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SRP54_ECOLI SRP54_ECOLI] Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY. Interaction with FtsY leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components.<ref>PMID:2171778</ref> <ref>PMID:1279430</ref> <ref>PMID:1331806</ref> <ref>PMID:9305630</ref> <ref>PMID:11735405</ref> <ref>PMID:11741850</ref> <ref>PMID:15140892</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hq/1hq1_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1hq1 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the endoplasmic reticulum in eukarya or to the inner membrane in prokarya. The crystal structure of the universally conserved RNA-protein core of the Escherichia coli SRP, refined here to 1.5 A resolution, revealed minor groove recognition of the 4.5 S RNA component by the M domain of the Ffh protein. Within the RNA, nucleotides comprising two phylogenetically conserved internal loops create a unique surface for protein recognition. To determine the energetic importance of conserved nucleotides for SRP assembly, we measured the affinity of the M domain for a series of RNA mutants. This analysis reveals how conserved nucleotides within the two internal loop motifs establish the architecture of the macromolecular interface and position essential functional groups for direct recognition by the protein.


===STRUCTURAL AND ENERGETIC ANALYSIS OF RNA RECOGNITION BY A UNIVERSALLY CONSERVED PROTEIN FROM THE SIGNAL RECOGNITION PARTICLE===
Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.,Batey RT, Sagar MB, Doudna JA J Mol Biol. 2001 Mar 16;307(1):229-46. PMID:11243816<ref>PMID:11243816</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1hq1" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_11243816}}, adds the Publication Abstract to the page
*[[Signal recognition particle protein|Signal recognition particle protein]]
(as it appears on PubMed at http://www.pubmed.gov), where 11243816 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_11243816}}
__TOC__
 
</StructureSection>
==About this Structure==
1HQ1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HQ1 OCA].
 
==Reference==
Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle., Batey RT, Sagar MB, Doudna JA, J Mol Biol. 2001 Mar 16;307(1):229-46. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11243816 11243816]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Batey, R T.]]
[[Category: Batey RT]]
[[Category: Doudna, J A.]]
[[Category: Doudna JA]]
[[Category: Sagar, M B.]]
[[Category: Sagar MB]]
[[Category: Double helix]]
[[Category: Internal loop]]
[[Category: Protein-rna complex]]
[[Category: Ribonucleoprotein]]
[[Category: Signal recognition particle]]
[[Category: Srp]]
[[Category: Tetraloop]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 08:31:16 2008''

Latest revision as of 09:14, 9 August 2023

STRUCTURAL AND ENERGETIC ANALYSIS OF RNA RECOGNITION BY A UNIVERSALLY CONSERVED PROTEIN FROM THE SIGNAL RECOGNITION PARTICLESTRUCTURAL AND ENERGETIC ANALYSIS OF RNA RECOGNITION BY A UNIVERSALLY CONSERVED PROTEIN FROM THE SIGNAL RECOGNITION PARTICLE

Structural highlights

1hq1 is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.52Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SRP54_ECOLI Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY. Interaction with FtsY leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components.[1] [2] [3] [4] [5] [6] [7]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the endoplasmic reticulum in eukarya or to the inner membrane in prokarya. The crystal structure of the universally conserved RNA-protein core of the Escherichia coli SRP, refined here to 1.5 A resolution, revealed minor groove recognition of the 4.5 S RNA component by the M domain of the Ffh protein. Within the RNA, nucleotides comprising two phylogenetically conserved internal loops create a unique surface for protein recognition. To determine the energetic importance of conserved nucleotides for SRP assembly, we measured the affinity of the M domain for a series of RNA mutants. This analysis reveals how conserved nucleotides within the two internal loop motifs establish the architecture of the macromolecular interface and position essential functional groups for direct recognition by the protein.

Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.,Batey RT, Sagar MB, Doudna JA J Mol Biol. 2001 Mar 16;307(1):229-46. PMID:11243816[8]

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

See Also

References

  1. ↑ Ribes V, Romisch K, Giner A, Dobberstein B, Tollervey D. E. coli 4.5S RNA is part of a ribonucleoprotein particle that has properties related to signal recognition particle. Cell. 1990 Nov 2;63(3):591-600. PMID:2171778
  2. ↑ Luirink J, High S, Wood H, Giner A, Tollervey D, Dobberstein B. Signal-sequence recognition by an Escherichia coli ribonucleoprotein complex. Nature. 1992 Oct 22;359(6397):741-3. PMID:1279430 doi:http://dx.doi.org/10.1038/359741a0
  3. ↑ Phillips GJ, Silhavy TJ. The E. coli ffh gene is necessary for viability and efficient protein export. Nature. 1992 Oct 22;359(6397):744-6. PMID:1331806 doi:http://dx.doi.org/10.1038/359744a0
  4. ↑ Powers T, Walter P. Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor. EMBO J. 1997 Aug 15;16(16):4880-6. PMID:9305630 doi:10.1093/emboj/16.16.4880
  5. ↑ Peluso P, Shan SO, Nock S, Herschlag D, Walter P. Role of SRP RNA in the GTPase cycles of Ffh and FtsY. Biochemistry. 2001 Dec 18;40(50):15224-33. PMID:11735405
  6. ↑ Tian H, Beckwith J. Genetic screen yields mutations in genes encoding all known components of the Escherichia coli signal recognition particle pathway. J Bacteriol. 2002 Jan;184(1):111-8. PMID:11741850
  7. ↑ Froderberg L, Houben EN, Baars L, Luirink J, de Gier JW. Targeting and translocation of two lipoproteins in Escherichia coli via the SRP/Sec/YidC pathway. J Biol Chem. 2004 Jul 23;279(30):31026-32. Epub 2004 May 12. PMID:15140892 doi:10.1074/jbc.M403229200
  8. ↑ Batey RT, Sagar MB, Doudna JA. Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. J Mol Biol. 2001 Mar 16;307(1):229-46. PMID:11243816 doi:http://dx.doi.org/10.1006/jmbi.2000.4454

1hq1, resolution 1.52Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1hq1&oldid=3822292"