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2hvq

From Proteopedia

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Structure of Adenylated full-length T4 RNA Ligase 2

Structural highlights

2hvq is a 1 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RLIG2_BPT4 Catalyzes intramolecular and intermolecular RNA strand joining (in vitro). May play a role in the repair of nicked RNA molecules.^[1] ^[2]

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

T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair.

RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.,Nandakumar J, Shuman S, Lima CD Cell. 2006 Oct 6;127(1):71-84. PMID:17018278^[3]

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

References

↑ Ho CK, Shuman S. Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains. Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12709-14. Epub 2002 Sep 12. PMID:12228725 doi:http://dx.doi.org/10.1073/pnas.192184699
↑ Nandakumar J, Shuman S, Lima CD. RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell. 2006 Oct 6;127(1):71-84. PMID:17018278 doi:10.1016/j.cell.2006.08.038
↑ Nandakumar J, Shuman S, Lima CD. RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell. 2006 Oct 6;127(1):71-84. PMID:17018278 doi:10.1016/j.cell.2006.08.038

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/2hvq"

Categories: Escherichia virus T4 | Large Structures | Lima CD | Nandakumar J

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2hvq.png|left|200px]]
-<!--
+==Structure of Adenylated full-length T4 RNA Ligase 2==
-The line below this paragraph, containing "STRUCTURE_2hvq", creates the "Structure Box" on the page.
+<StructureSection load='2hvq' size='340' side='right'caption='[[2hvq]], [[Resolution|resolution]] 2.40&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'>[[2hvq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HVQ 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]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APK:5-O-[(S)-{[(5S)-5-AMINO-6-OXOHEXYL]AMINO}(HYDROXY)PHOSPHORYL]ADENOSINE'>APK</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_2hvq|  PDB=2hvq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hvq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvq OCA], [https://pdbe.org/2hvq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hvq RCSB], [https://www.ebi.ac.uk/pdbsum/2hvq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hvq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RLIG2_BPT4 RLIG2_BPT4] Catalyzes intramolecular and intermolecular RNA strand joining (in vitro). May play a role in the repair of nicked RNA molecules.<ref>PMID:12228725</ref> <ref>PMID:17018278</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/hv/2hvq_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=2hvq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair.
-===Structure of Adenylated full-length T4 RNA Ligase 2===
+RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.,Nandakumar J, Shuman S, Lima CD Cell. 2006 Oct 6;127(1):71-84. PMID:17018278<ref>PMID:17018278</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2hvq" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17018278}}, adds the Publication Abstract to the page
+*[[RNA ligase|RNA ligase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17018278 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17018278}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia virus T4]]
-HVQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVQ OCA].
+[[Category: Large Structures]]
+[[Category: Lima CD]]
-==Reference==
+[[Category: Nandakumar J]]
-RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward., Nandakumar J, Shuman S, Lima CD, Cell. 2006 Oct 6;127(1):71-84. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17018278 17018278]
-[[Category: Enterobacteria phage t4]]
-[[Category: Single protein]]
-[[Category: Lima, C D.]]
-[[Category: Nandakumar, J.]]
-[[Category: Ligase]]
-[[Category: Lysine adenylate]]
-[[Category: Rna]]
-[[Category: T4]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 06:17:02 2008''

2hvq

From Proteopedia

Current revision

Structure of Adenylated full-length T4 RNA Ligase 2

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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