2gaf

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of the Vaccinia Polyadenylate Polymerase Heterodimer (apo form)

Structural highlights

2gaf is a 2 chain structure with sequence from Vaccinia virus. 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

Q1PIV4_9POXV Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase OPG063 that creates mRNA's poly(A) tail. In the presence of OPG102, OPG063 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.[ARBA:ARBA00034661][PIRNR:PIRNR003726]

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

Polyadenylation of mRNAs in poxviruses, crucial for virion maturation, is carried out by a poly(A) polymerase heterodimer composed of a catalytic component, VP55, and a processivity factor, VP39. The ATP-gamma-S bound and unbound crystal structures of the vaccinia polymerase reveal an unusual architecture for VP55 that comprises of N-terminal, central or catalytic, and C-terminal domains with different topologies and that differs from many polymerases, including the eukaryotic poly(A) polymerases. Residues in the active site of VP55, located between the catalytic and C-terminal domains, make specific interactions with the adenine of the ATP analog, establishing the molecular basis of ATP recognition. VP55's concave surface docks the globular VP39. A model for RNA primer binding that involves all three VP55 domains and VP39 is proposed. The model supports biochemical evidence that VP39 functions as a processivity factor by partially enclosing the RNA primer at the heterodimer interface.

Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity.,Moure CM, Bowman BR, Gershon PD, Quiocho FA Mol Cell. 2006 May 5;22(3):339-49. PMID:16678106^[1]

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

References

↑ Moure CM, Bowman BR, Gershon PD, Quiocho FA. Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity. Mol Cell. 2006 May 5;22(3):339-49. PMID:16678106 doi:10.1016/j.molcel.2006.03.015

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/2gaf"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2gaf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GAF FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ga9|2ga9]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/mRNA_(nucleoside-2'-O)-methyltransferase mRNA (nucleoside-2'-O)-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.57 2.1.1.57] </span></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=2gaf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gaf OCA], [https://pdbe.org/2gaf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gaf RCSB], [https://www.ebi.ac.uk/pdbsum/2gaf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gaf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MCE_VACCW MCE_VACCW]] Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase VP55 that creates mRNA's poly(A) tail. In the presence of VP39, VP55 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.<ref>PMID:1313572</ref> <ref>PMID:1670500</ref> <ref>PMID:12359447</ref>  [[https://www.uniprot.org/uniprot/PAP1_VACCW PAP1_VACCW]] Polymerase that creates the 3'-poly(A) tail of mRNA's.
+[https://www.uniprot.org/uniprot/Q1PIV4_9POXV Q1PIV4_9POXV] Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase OPG063 that creates mRNA's poly(A) tail. In the presence of OPG102, OPG063 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.[ARBA:ARBA00034661][PIRNR:PIRNR003726]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 16: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/2gaf_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Poly(A) Polymerase|Poly(A) Polymerase]]
+*[[Poly(A) polymerase 3D structures|Poly(A) polymerase 3D structures]]
 == References ==
 <references/>
@@ Line 39: / Line 38: @@
 [[Category: Large Structures]]
 [[Category: Vaccinia virus]]
-[[Category: Bowman, B R]]
+[[Category: Bowman BR]]
-[[Category: Gershon, P D]]
+[[Category: Gershon PD]]
-[[Category: Moure, C M]]
+[[Category: Moure CM]]
-[[Category: Quiocho, F A]]
+[[Category: Quiocho FA]]
-[[Category: Heterodimer]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Polyadenylate polymerase]]
-[[Category: Pox virus]]
-[[Category: Processivity]]
-[[Category: Transferase]]

2gaf

From Proteopedia

Current revision

Crystal Structure of the Vaccinia Polyadenylate Polymerase Heterodimer (apo form)

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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