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1rgc

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[[Image:1rgc.gif|left|200px]]<br /><applet load="1rgc" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rgc, resolution 2.0&Aring;" />
 
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'''THE COMPLEX BETWEEN RIBONUCLEASE T1 AND 3'-GUANYLIC ACID SUGGESTS GEOMETRY OF ENZYMATIC REACTION PATH. AN X-RAY STUDY'''<br />
 
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==Overview==
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==THE COMPLEX BETWEEN RIBONUCLEASE T1 AND 3'-GUANYLIC ACID SUGGESTS GEOMETRY OF ENZYMATIC REACTION PATH. AN X-RAY STUDY==
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The crystal structure of the complex between ribonuclease T1 and 3'GMP suggests that (a) a substrate GpN is bound to the active site of ribonuclease T1 in a conformation that actively supports the catalytic process, (b) the reaction occurs in an in-line process, (c) His40 N epsilon H+ activates O2'-H, (d) Glu58 carboxylate acts as base and His92 N epsilon H+ as acid in a general acid-base catalysis. The crystals have the monoclinic space group P2(1), a = 4.968 nm, b = 4.833 nm, c = 4.048 nm, beta = 90.62 degrees with two molecules in the asymmetric unit. The structure was determined by molecular replacement and refined to R = 15.3% with 11,338 data &gt; or = 1 sigma (Fo) in the resolution range 1.0-0.2 nm; this includes 180 water molecules and two Ca2+. The structure of ribonuclease T1 is as previously observed. 3'GMP is bound in syn conformation; guanine is located in the specific recognition site, the ribose adopts C4'-exo puckering, the ribose phosphate is extended with torsion angle epsilon in trans. The O2'-H group is activated by accepting and donating hydrogen bonds from His40 N epsilon H+ and to Glu58 O epsilon 1; the phosphate is hydrogen bonded to Glu58 O epsilon 2H, Arg77 N epsilon H+ and N eta 2H+, Tyr38 O eta H, His92 N eta H+. The conformation of ribose phosphate is such that O2' is at a distance of 0.31 nm from phosphorus, and opposite the P-OP3 bond which accepts a hydrogen bond from His92 N epsilon H+; we infer from a model building study that this bond is equivalent to the scissile P-O5' in a substrate GpN.
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<StructureSection load='1rgc' size='340' side='right'caption='[[1rgc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rgc]] is a 2 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=1RGC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RGC FirstGlance]. <br>
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rgc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rgc OCA], [https://pdbe.org/1rgc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rgc RCSB], [https://www.ebi.ac.uk/pdbsum/1rgc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rgc ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rg/1rgc_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1rgc ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1RGC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=3GP:'>3GP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RGC OCA].
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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The complex between ribonuclease T1 and 3'GMP suggests geometry of enzymic reaction path. An X-ray study., Heydenreich A, Koellner G, Choe HW, Cordes F, Kisker C, Schindelin H, Adamiak R, Hahn U, Saenger W, Eur J Biochem. 1993 Dec 15;218(3):1005-12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8281918 8281918]
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[[Category: Aspergillus oryzae]]
[[Category: Aspergillus oryzae]]
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[[Category: Ribonuclease T(1)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Adamiak R]]
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[[Category: Adamiak, R.]]
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[[Category: Choe HW]]
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[[Category: Choe, H W.]]
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[[Category: Cordes F]]
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[[Category: Cordes, F.]]
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[[Category: Hahn U]]
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[[Category: Hahn, U.]]
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[[Category: Heydenreich A]]
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[[Category: Heydenreich, A.]]
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[[Category: Kisker C]]
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[[Category: Kisker, C.]]
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[[Category: Koellner G]]
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[[Category: Koellner, G.]]
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[[Category: Saenger W]]
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[[Category: Saenger, W.]]
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[[Category: Schindelin H]]
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[[Category: Schindelin, H.]]
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[[Category: 3GP]]
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[[Category: CA]]
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[[Category: hydrolase(endoribonuclease)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:50:34 2008''
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Current revision

THE COMPLEX BETWEEN RIBONUCLEASE T1 AND 3'-GUANYLIC ACID SUGGESTS GEOMETRY OF ENZYMATIC REACTION PATH. AN X-RAY STUDY

PDB ID 1rgc

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