2hz7

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the Glutaminyl-tRNA synthetase from Deinococcus radiodurans

Structural highlights

2hz7 is a 1 chain structure with sequence from Deinococcus radiodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYQ_DEIRA

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

Glutaminyl-tRNA synthetase from Deinococcus radiodurans possesses a C-terminal extension of 215 residues appending the anticodon-binding domain. This domain constitutes a paralog of the Yqey protein present in various organisms and part of it is present in the C-terminal end of the GatB subunit of GatCAB, a partner of the indirect pathway of Gln-tRNA(Gln) formation. To analyze the peculiarities of the structure-function relationship of this GlnRS related to the Yqey domain, a structure of the protein was solved from crystals diffracting at 2.3 A and a docking model of the synthetase complexed to tRNA(Gln) constructed. The comparison of the modeled complex with the structure of the E. coli complex reveals that all residues of E. coli GlnRS contacting tRNA(Gln) are conserved in D. radiodurans GlnRS, leaving the functional role of the Yqey domain puzzling. Kinetic investigations and tRNA-binding experiments of full length and Yqey-truncated GlnRSs reveal that the Yqey domain is involved in tRNA(Gln) recognition. They demonstrate that Yqey plays the role of an affinity-enhancer of GlnRS for tRNA(Gln) acting only in cis. However, the presence of Yqey in free state in organisms lacking GlnRS, suggests that this domain may exert additional cellular functions.

Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation.,Deniziak M, Sauter C, Becker HD, Paulus CA, Giege R, Kern D Nucleic Acids Res. 2007;35(5):1421-31. Epub 2007 Feb 6. PMID:17284460^[1]

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

References

↑ Deniziak M, Sauter C, Becker HD, Paulus CA, Giege R, Kern D. Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation. Nucleic Acids Res. 2007;35(5):1421-31. Epub 2007 Feb 6. PMID:17284460 doi:10.1093/nar/gkl1164

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2hz7"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2hz7.png|left|200px]]
-<!--
+==Crystal structure of the Glutaminyl-tRNA synthetase from Deinococcus radiodurans==
-The line below this paragraph, containing "STRUCTURE_2hz7", creates the "Structure Box" on the page.
+<StructureSection load='2hz7' size='340' side='right'caption='[[2hz7]], [[Resolution|resolution]] 2.30&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'>[[2hz7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HZ7 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]] 2.3&#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=2hz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hz7 OCA], [https://pdbe.org/2hz7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hz7 RCSB], [https://www.ebi.ac.uk/pdbsum/2hz7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hz7 ProSAT]</span></td></tr>
-{{STRUCTURE_2hz7|  PDB=2hz7  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYQ_DEIRA SYQ_DEIRA]
+== 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/hz/2hz7_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=2hz7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Glutaminyl-tRNA synthetase from Deinococcus radiodurans possesses a C-terminal extension of 215 residues appending the anticodon-binding domain. This domain constitutes a paralog of the Yqey protein present in various organisms and part of it is present in the C-terminal end of the GatB subunit of GatCAB, a partner of the indirect pathway of Gln-tRNA(Gln) formation. To analyze the peculiarities of the structure-function relationship of this GlnRS related to the Yqey domain, a structure of the protein was solved from crystals diffracting at 2.3 A and a docking model of the synthetase complexed to tRNA(Gln) constructed. The comparison of the modeled complex with the structure of the E. coli complex reveals that all residues of E. coli GlnRS contacting tRNA(Gln) are conserved in D. radiodurans GlnRS, leaving the functional role of the Yqey domain puzzling. Kinetic investigations and tRNA-binding experiments of full length and Yqey-truncated GlnRSs reveal that the Yqey domain is involved in tRNA(Gln) recognition. They demonstrate that Yqey plays the role of an affinity-enhancer of GlnRS for tRNA(Gln) acting only in cis. However, the presence of Yqey in free state in organisms lacking GlnRS, suggests that this domain may exert additional cellular functions.
-===Crystal structure of the Glutaminyl-tRNA synthetase from Deinococcus radiodurans===
+Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation.,Deniziak M, Sauter C, Becker HD, Paulus CA, Giege R, Kern D Nucleic Acids Res. 2007;35(5):1421-31. Epub 2007 Feb 6. PMID:17284460<ref>PMID:17284460</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2hz7" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17284460}}, adds the Publication Abstract to the page
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17284460 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17284460}}
+__TOC__
+</StructureSection>
-==About this Structure==
-HZ7 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZ7 OCA].
-==Reference==
-Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation., Deniziak M, Sauter C, Becker HD, Paulus CA, Giege R, Kern D, Nucleic Acids Res. 2007;35(5):1421-31. Epub 2007 Feb 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17284460 17284460]
-Crystallization and preliminary X-ray characterization of the atypical glutaminyl-tRNA synthetase from Deinococcus radiodurans., Deniziak MA, Sauter C, Becker HD, Giege R, Kern D, Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 2):2361-3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15614972 15614972]
 [[Category: Deinococcus radiodurans]]
-[[Category: Glutamine--tRNA ligase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Becker HD]]
-[[Category: Becker, H D.]]
+[[Category: Deniziak M]]
-[[Category: Deniziak, M.]]
+[[Category: Giege R]]
-[[Category: Giege, R.]]
+[[Category: Kern D]]
-[[Category: Kern, D.]]
+[[Category: Paulus C]]
-[[Category: Paulus, C.]]
+[[Category: Sauter C]]
-[[Category: Sauter, C.]]
-[[Category: Class i aminoacyl-trna synthetase]]
-[[Category: Glnrs core]]
-[[Category: Rossmann fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 21:33:05 2008''

2hz7

From Proteopedia

Current revision

Crystal structure of the Glutaminyl-tRNA synthetase from Deinococcus radiodurans

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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