2f91: Difference between revisions

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-{{Seed}}
-[[Image:2f91.png|left|200px]]
-<!--
+==1.2A resolution structure of a crayfish trypsin complexed with a peptide inhibitor, SGTI==
-The line below this paragraph, containing "STRUCTURE_2f91", creates the "Structure Box" on the page.
+<StructureSection load='2f91' size='340' side='right'caption='[[2f91]], [[Resolution|resolution]] 1.20&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'>[[2f91]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Astacus_leptodactylus Astacus leptodactylus] and [https://en.wikipedia.org/wiki/Schistocerca_gregaria Schistocerca gregaria]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1yr4 1yr4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F91 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F91 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]] 1.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-{{STRUCTURE_2f91|  PDB=2f91  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f91 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f91 OCA], [https://pdbe.org/2f91 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f91 RCSB], [https://www.ebi.ac.uk/pdbsum/2f91 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f91 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q52V24_ASTLP Q52V24_ASTLP]
+== 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/f9/2f91_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=2f91 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Atomic resolution (&lt;or=1.2 A) serine protease intermediate structures revealed that the strength of the hydrogen bonds between the enzyme and the substrate changed during catalysis. The well-conserved hydrogen bonds of antiparallel beta-sheet between the enzyme and the substrate become significantly shorter in the transition from a Michaelis complex analogue (Pontastacus leptodactylus (narrow-fingered crayfish) trypsin (CFT) in complex with Schistocerca gregaria (desert locust) trypsin inhibitor (SGTI) at 1.2 A resolution) to an acyl-enzyme intermediate (N-acetyl-Asn-Pro-Ile acyl-enzyme intermediate of porcine pancreatic elastase at 0.95 A resolution) presumably synchronously with the nucleophilic attack on the carbonyl carbon atom of the scissile peptide bond. This is interpreted as an active mechanism that utilizes the energy released from the stronger hydrogen bonds to overcome the energetic barrier of the nucleophilic attack by the hydroxyl group of the catalytic serine. In the CFT:SGTI complex this hydrogen bond shortening may be hindered by the 27I-32I disulfide bridge and Asn-15I of SGTI. The position of the catalytic histidine changes slightly as it adapts to the different nucleophilic attacker during the transition from the Michaelis complex to the acyl-enzyme state, and simultaneously its interaction with Asp-102 and Ser-214 becomes stronger. The oxyanion hole hydrogen bonds provide additional stabilization for acyl-ester bond in the acyl-enzyme than for scissile peptide bond of the Michaelis complex. Significant deviation from planarity is not observed in the reactive bonds of either the Michaelis complex or the acyl-enzyme. In the Michaelis complex the electron distribution of the carbonyl bond is distorted toward the oxygen atom compared to other peptide bonds in the structure, which indicates the polarization effect of the oxyanion hole.
-===1.2A resolution structure of a crayfish trypsin complexed with a peptide inhibitor, SGTI===
+Enzyme:substrate hydrogen bond shortening during the acylation phase of serine protease catalysis.,Fodor K, Harmat V, Neutze R, Szilagyi L, Graf L, Katona G Biochemistry. 2006 Feb 21;45(7):2114-21. PMID:16475800<ref>PMID:16475800</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2f91" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16475800}}, adds the Publication Abstract to the page
+*[[Trypsin 3D structures|Trypsin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16475800 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16475800}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Astacus leptodactylus]]
-F91 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Pontastacus_leptodactylus Pontastacus leptodactylus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1yr4 1yr4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F91 OCA].
+[[Category: Large Structures]]
+[[Category: Schistocerca gregaria]]
-==Reference==
+[[Category: Antal J]]
-<ref group="xtra">PMID:16475800</ref><ref group="xtra">PMID:15922357</ref><references group="xtra"/>
+[[Category: Fodor K]]
-[[Category: Pontastacus leptodactylus]]
+[[Category: Graf L]]
-[[Category: Trypsin]]
+[[Category: Harmat V]]
-[[Category: Antal, J.]]
+[[Category: Hetenyi C]]
-[[Category: Fodor, K.]]
+[[Category: Kardos J]]
-[[Category: Graf, L.]]
+[[Category: Katona G]]
-[[Category: Harmat, V.]]
+[[Category: Patthy A]]
-[[Category: Hetenyi, C.]]
+[[Category: Perczel A]]
-[[Category: Kardos, J.]]
-[[Category: Katona, G.]]
-[[Category: Patthy, A.]]
-[[Category: Perczel, A.]]
-[[Category: Atomic resolution]]
-[[Category: Canonical inhibitor]]
-[[Category: Serine protease]]
-[[Category: Trypsin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:58:36 2009''