This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1fus

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:16, 27 March 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1fus.jpg|left|200px]]
 
-
{{Structure
+
==CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ITS FREE FORM AND IN COMPLEX WITH 2'GMP==
-
|PDB= 1fus |SIZE=350|CAPTION= <scene name='initialview01'>1fus</scene>, resolution 1.3&Aring;
+
<StructureSection load='1fus' size='340' side='right'caption='[[1fus]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>
+
<table><tr><td colspan='2'>[[1fus]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_fujikuroi Fusarium fujikuroi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FUS FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[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] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fus OCA], [https://pdbe.org/1fus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fus RCSB], [https://www.ebi.ac.uk/pdbsum/1fus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fus ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fus OCA], [http://www.ebi.ac.uk/pdbsum/1fus PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fus RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/RNF1_GIBFU RNF1_GIBFU]
 +
== 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/fu/1fus_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=1fus ConSurf].
 +
<div style="clear:both"></div>
-
'''CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ITS FREE FORM AND IN COMPLEX WITH 2'GMP'''
+
==See Also==
-
 
+
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
RNase F1, a guanine-specific ribonuclease from Fusarium moniliforme, was crystallized in two different forms, in the absence of an inhibitor and in the presence of 2'GMP. The crystal structure of the RNase F1 free form was solved by the molecular replacement method, using the co-ordinates of the RNase T1 complex with 2'GMP, and was refined to a final R-factor of 18.7%, using the data extended to 1.3 A resolution. For the crystal structure of the RNase F1 complex with 2'GMP, the solution of the molecular replacement method was obtained on the basis of the co-ordinates of the RNase F1 free form, and was refined to a final R-factor of 16.8%, using the data up to 2 A resolution. The two crystal structures of the RNase F1 free form and the complex with 2'GMP are very similar to each other as reflected by a small root-mean-square displacement (r.m.s.d.) value of 0.43 A for all C alpha atoms. The main differences between the two structures are associated with binding of 2'GMP in the substrate recognition site in the loop between Tyr42 and Glu46. A structural comparison between RNase F1 and RNase T1 shows a substantial similarity between all the C alpha atoms, as evidenced by a r.m.s.d. value of 1.4 A. The loop from residues 32 to 38 was strikingly different between these two enzymes, in both its conformation and its hydrogen bonding schemes. The side-chain of a catalytically active residue, His92, is shifted away from the catalytic site in RNase F1 by 1.3 A and 0.85 A with respect to the corresponding positions in the RNase T1 free form and in the RNase T1 complex with 2'GMP, respectively. In the RNase F1 complex, the guanine base of 2'GMP has a syn conformation about the glycosyl bond, and the furanose ring assumes a 3'-exo pucker, which is different from that found in the complex with RNase T1. In the catalytic site of the RNase F1 complex with 2'GMP, one water molecule was observed, which bridges the phosphate oxygen atoms of 2'GMP and the side-chains of the catalytically important residues, His92 and Arg77, through hydrogen bonds. A water molecule occupying the same position was found in the RNase F1 free form. The significance of this water molecule in the hydrolytic reaction is discussed.
+
[[Category: Fusarium fujikuroi]]
-
 
+
[[Category: Large Structures]]
-
==About this Structure==
+
[[Category: Ishikawa K]]
-
1FUS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gibberella_fujikuroi Gibberella fujikuroi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FUS OCA].
+
[[Category: Katayanagi K]]
-
 
+
[[Category: Morikawa K]]
-
==Reference==
+
[[Category: Vassylyev DG]]
-
Crystal structures of ribonuclease F1 of Fusarium moniliforme in its free form and in complex with 2'GMP., Vassylyev DG, Katayanagi K, Ishikawa K, Tsujimoto-Hirano M, Danno M, Pahler A, Matsumoto O, Matsushima M, Yoshida H, Morikawa K, J Mol Biol. 1993 Apr 5;230(3):979-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8386773 8386773]
+
-
[[Category: Gibberella fujikuroi]]
+
-
[[Category: Ribonuclease T(1)]]
+
-
[[Category: Single protein]]
+
-
[[Category: Ishikawa, K.]]
+
-
[[Category: Katayanagi, K.]]
+
-
[[Category: Morikawa, K.]]
+
-
[[Category: Vassylyev, D G.]]
+
-
[[Category: hydrolase(endoribonuclease)]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:30:40 2008''
+

Current revision

CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ITS FREE FORM AND IN COMPLEX WITH 2'GMP

PDB ID 1fus

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1fus"
Personal tools