5hoh: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:5hoh.gif|left|200px]]


{{Structure
==RIBONUCLEASE T1 (ASN9ALA/THR93ALA DOUBLEMUTANT) COMPLEXED WITH 2'GMP==
|PDB= 5hoh |SIZE=350|CAPTION= <scene name='initialview01'>5hoh</scene>, resolution 2.00&Aring;
<StructureSection load='5hoh' size='340' side='right'caption='[[5hoh]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=2GP:GUANOSINE-2'-MONOPHOSPHATE'>2GP</scene>
<table><tr><td colspan='2'>[[5hoh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HOH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HOH FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3]  
</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&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=5hoh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hoh OCA], [https://pdbe.org/5hoh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hoh RCSB], [https://www.ebi.ac.uk/pdbsum/5hoh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hoh ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR]
== 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/ho/5hoh_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=5hoh ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The reoccurrence of water molecules in crystal structures of RNase T1 was investigated. Five waters were found to be invariant in RNase T1 as well as in six other related fungal RNases. The structural, dynamical, and functional characteristics of one of these conserved hydration sites (WAT1) were analyzed by protein engineering, X-ray crystallography, and (17)O and 2H nuclear magnetic relaxation dispersion (NMRD). The position of WAT1 and its surrounding hydrogen bond network are unaffected by deletions of two neighboring side chains. In the mutant Thr93Gln, the Gln93N epsilon2 nitrogen replaces WAT1 and participates in a similar hydrogen bond network involving Cys6, Asn9, Asp76, and Thr91. The ability of WAT1 to form four hydrogen bonds may explain why evolution has preserved a water molecule, rather than a side-chain atom, at the center of this intricate hydrogen bond network. Comparison of the (17)O NMRD profiles from wild-type and Thr93Gln RNase T1 yield a mean residence time of 7 ns at 27 degrees C and an orientational order parameter of 0.45. The effects of mutations around WAT1 on the kinetic parameters of RNase T1 are small but significant and probably relate to the dynamics of the active site.


'''RIBONUCLEASE T1 (ASN9ALA/THR93ALA DOUBLEMUTANT) COMPLEXED WITH 2'GMP'''
Dissection of the structural and functional role of a conserved hydration site in RNase T1.,Langhorst U, Loris R, Denisov VP, Doumen J, Roose P, Maes D, Halle B, Steyaert J Protein Sci. 1999 Apr;8(4):722-30. PMID:10211818<ref>PMID:10211818</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5hoh" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The reoccurrence of water molecules in crystal structures of RNase T1 was investigated. Five waters were found to be invariant in RNase T1 as well as in six other related fungal RNases. The structural, dynamical, and functional characteristics of one of these conserved hydration sites (WAT1) were analyzed by protein engineering, X-ray crystallography, and (17)O and 2H nuclear magnetic relaxation dispersion (NMRD). The position of WAT1 and its surrounding hydrogen bond network are unaffected by deletions of two neighboring side chains. In the mutant Thr93Gln, the Gln93N epsilon2 nitrogen replaces WAT1 and participates in a similar hydrogen bond network involving Cys6, Asn9, Asp76, and Thr91. The ability of WAT1 to form four hydrogen bonds may explain why evolution has preserved a water molecule, rather than a side-chain atom, at the center of this intricate hydrogen bond network. Comparison of the (17)O NMRD profiles from wild-type and Thr93Gln RNase T1 yield a mean residence time of 7 ns at 27 degrees C and an orientational order parameter of 0.45. The effects of mutations around WAT1 on the kinetic parameters of RNase T1 are small but significant and probably relate to the dynamics of the active site.
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 
== References ==
==About this Structure==
<references/>
5HOH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HOH OCA].
__TOC__
 
</StructureSection>
==Reference==
Dissection of the structural and functional role of a conserved hydration site in RNase T1., Langhorst U, Loris R, Denisov VP, Doumen J, Roose P, Maes D, Halle B, Steyaert J, Protein Sci. 1999 Apr;8(4):722-30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10211818 10211818]
[[Category: Aspergillus oryzae]]
[[Category: Aspergillus oryzae]]
[[Category: Ribonuclease T(1)]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Denisov VP]]
[[Category: Denisov, V P.]]
[[Category: Doumen J]]
[[Category: Doumen, J.]]
[[Category: Halle B]]
[[Category: Halle, B.]]
[[Category: Langhorst U]]
[[Category: Langhorst, U.]]
[[Category: Loris R]]
[[Category: Loris, R.]]
[[Category: Maes D]]
[[Category: Maes, D.]]
[[Category: Roose P]]
[[Category: Roose, P.]]
[[Category: Steyaert J]]
[[Category: Steyaert, J.]]
[[Category: 2GP]]
[[Category: CA]]
[[Category: endonuclease]]
[[Category: endoribonuclease]]
[[Category: hydrolase]]
[[Category: ribonuclease]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:12:15 2008''

Latest revision as of 13:41, 30 October 2024

RIBONUCLEASE T1 (ASN9ALA/THR93ALA DOUBLEMUTANT) COMPLEXED WITH 2'GMPRIBONUCLEASE T1 (ASN9ALA/THR93ALA DOUBLEMUTANT) COMPLEXED WITH 2'GMP

Structural highlights

5hoh is a 4 chain structure with sequence from Aspergillus oryzae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNT1_ASPOR

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 reoccurrence of water molecules in crystal structures of RNase T1 was investigated. Five waters were found to be invariant in RNase T1 as well as in six other related fungal RNases. The structural, dynamical, and functional characteristics of one of these conserved hydration sites (WAT1) were analyzed by protein engineering, X-ray crystallography, and (17)O and 2H nuclear magnetic relaxation dispersion (NMRD). The position of WAT1 and its surrounding hydrogen bond network are unaffected by deletions of two neighboring side chains. In the mutant Thr93Gln, the Gln93N epsilon2 nitrogen replaces WAT1 and participates in a similar hydrogen bond network involving Cys6, Asn9, Asp76, and Thr91. The ability of WAT1 to form four hydrogen bonds may explain why evolution has preserved a water molecule, rather than a side-chain atom, at the center of this intricate hydrogen bond network. Comparison of the (17)O NMRD profiles from wild-type and Thr93Gln RNase T1 yield a mean residence time of 7 ns at 27 degrees C and an orientational order parameter of 0.45. The effects of mutations around WAT1 on the kinetic parameters of RNase T1 are small but significant and probably relate to the dynamics of the active site.

Dissection of the structural and functional role of a conserved hydration site in RNase T1.,Langhorst U, Loris R, Denisov VP, Doumen J, Roose P, Maes D, Halle B, Steyaert J Protein Sci. 1999 Apr;8(4):722-30. PMID:10211818[1]

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

See Also

References

  1. ↑ Langhorst U, Loris R, Denisov VP, Doumen J, Roose P, Maes D, Halle B, Steyaert J. Dissection of the structural and functional role of a conserved hydration site in RNase T1. Protein Sci. 1999 Apr;8(4):722-30. PMID:10211818

5hoh, resolution 2.00Å

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=5hoh&oldid=4199258"