2qca: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:2qca.png|left|200px]]


<!--
==A New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphate==
The line below this paragraph, containing "STRUCTURE_2qca", creates the "Structure Box" on the page.
<StructureSection load='2qca' size='340' side='right'caption='[[2qca]], [[Resolution|resolution]] 1.33&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'>[[2qca]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QCA 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]] 1.33&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene></td></tr>
{{STRUCTURE_2qca|  PDB=2qca  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qca OCA], [https://pdbe.org/2qca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qca RCSB], [https://www.ebi.ac.uk/pdbsum/2qca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qca ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</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/qc/2qca_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2qca ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structure of bovine pancreatic RNase A has been determined in complex with 2'-deoxyguanosine-5'-monophosphate (dGMP) at 1.33 A resolution at room temperature in a previously unreported unit cell belonging to space group P3(1). There are two molecules of nucleotide per enzyme molecule, one of which lies in the active-site cleft in the productive binding mode, whilst the guanine base of the other dGMP occupies the pyrimidine-specific binding site in a nonproductive mode such that it forms hydrogen bonds to the phosphate group of the first dGMP. This is the first RNase A structure containing a guanine base in the B2 binding site. Each dGMP molecule is involved in intermolecular interactions with adjacent RNase A molecules in the lattice and the two nucleotides appear to direct the formation of the crystal lattice. Because GMP may be produced during degradation of RNA, this association could represent an inhibitor complex and thereby affect the observed enzyme kinetics.


===A New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphate===
A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate.,Larson SB, Day JS, Cudney R, McPherson A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Sep 1;63(Pt, 9):728-33. Epub 2007 Aug 31. PMID:17768339<ref>PMID:17768339</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2qca" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17768339}}, adds the Publication Abstract to the page
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17768339 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17768339}}
__TOC__
 
</StructureSection>
==About this Structure==
2QCA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QCA OCA].
 
==Reference==
A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate., Larson SB, Day JS, Cudney R, McPherson A, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Sep 1;63(Pt, 9):728-33. Epub 2007 Aug 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17768339 17768339]
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Pancreatic ribonuclease]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Cudney R]]
[[Category: CHTSB, Center for High-Throughput Structural Biology.]]
[[Category: Day JS]]
[[Category: Cudney, R.]]
[[Category: Larson SB]]
[[Category: Day, J S.]]
[[Category: McPherson A]]
[[Category: Larson, S B.]]
[[Category: McPherson, A.]]
[[Category: Center for high-throughput structural biology]]
[[Category: Chtsb]]
[[Category: Hydrolase]]
[[Category: Protein structure initiative]]
[[Category: Protein-nucleotide complex]]
[[Category: Psi-2]]
[[Category: Ribonuclease]]
[[Category: Structural genomic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 12:09:29 2008''

Latest revision as of 04:21, 21 November 2024

A New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphateA New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphate

Structural highlights

2qca is a 1 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.33Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNAS1_BOVIN Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.[1]

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 structure of bovine pancreatic RNase A has been determined in complex with 2'-deoxyguanosine-5'-monophosphate (dGMP) at 1.33 A resolution at room temperature in a previously unreported unit cell belonging to space group P3(1). There are two molecules of nucleotide per enzyme molecule, one of which lies in the active-site cleft in the productive binding mode, whilst the guanine base of the other dGMP occupies the pyrimidine-specific binding site in a nonproductive mode such that it forms hydrogen bonds to the phosphate group of the first dGMP. This is the first RNase A structure containing a guanine base in the B2 binding site. Each dGMP molecule is involved in intermolecular interactions with adjacent RNase A molecules in the lattice and the two nucleotides appear to direct the formation of the crystal lattice. Because GMP may be produced during degradation of RNA, this association could represent an inhibitor complex and thereby affect the observed enzyme kinetics.

A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate.,Larson SB, Day JS, Cudney R, McPherson A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Sep 1;63(Pt, 9):728-33. Epub 2007 Aug 31. PMID:17768339[2]

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

See Also

References

  1. ↑ delCardayre SB, Ribo M, Yokel EM, Quirk DJ, Rutter WJ, Raines RT. Engineering ribonuclease A: production, purification and characterization of wild-type enzyme and mutants at Gln11. Protein Eng. 1995 Mar;8(3):261-73. PMID:7479688
  2. ↑ Larson SB, Day JS, Cudney R, McPherson A. A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Sep 1;63(Pt, 9):728-33. Epub 2007 Aug 31. PMID:17768339 doi:10.1107/S1744309107039565

2qca, resolution 1.33Å

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=2qca&oldid=4202554"