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New page: left|200px<br /><applet load="1ic6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ic6, resolution 0.98Å" /> '''STRUCTURE OF A SERIN... |
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== | ==STRUCTURE OF A SERINE PROTEASE PROTEINASE K FROM TRITIRACHIUM ALBUM LIMBER AT 0.98 A RESOLUTION== | ||
X-ray diffraction data at atomic resolution to 0.98 A with 136 380 | <StructureSection load='1ic6' size='340' side='right'caption='[[1ic6]], [[Resolution|resolution]] 0.98Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1ic6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Parengyodontium_album Parengyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IC6 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.98Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=1ic6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ic6 OCA], [https://pdbe.org/1ic6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ic6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ic6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ic6 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PRTK_PARAQ PRTK_PARAQ] Hydrolyzes keratin at aromatic and hydrophobic residues. | |||
== 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/ic/1ic6_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=1ic6 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
X-ray diffraction data at atomic resolution to 0.98 A with 136 380 observed unique reflections were collected using a high quality proteinase K crystals grown under microgravity conditions and cryocooled. The structure has been refined anisotropically with REFMAC and SHELX-97 with R-factors of 11.4 and 12.8%, and R(free)-factors of 12.4 and 13.5%, respectively. The refined model coordinates have an overall rms shifts of 0.23 A relative to the same structure determined at room temperature at 1.5 A resolution. Several regions of the main chain and the side chains, which were not observed earlier have been seen more clearly. For example, amino acid 207, which was reported earlier as Ser has been clearly identified as Asp. Furthermore, side-chain disorders of 8 of 279 residues in the polypeptide have been identified. Hydrogen atoms appear as significant peaks in the F(o) - F(c) difference electron density map accounting for an estimated 46% of all hydrogen atoms at 2sigma level. Furthermore, the carbon, nitrogen, and oxygen atoms can be differentiated clearly in the electron density maps. Hydrogen bonds are clearly identified in the serine protease catalytic triad (Ser-His-Asp). Furthermore, electron density is observed for an unusual, short hydrogen bond between aspartic acid and histidine in the catalytic triad. The short hydrogen bond, designated "catalytic hydrogen bond", occurs as part of an elaborate hydrogen bond network, involving Asp of the catalytic triad. Though unusual, these features seem to be conserved in other serine proteases. Finally there are clear electron density peaks for the hydrogen atoms associated with the Ogamma of Ser 224 and Ndelta1 of His 69. | |||
Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 A resolution.,Betzel C, Gourinath S, Kumar P, Kaur P, Perbandt M, Eschenburg S, Singh TP Biochemistry. 2001 Mar 13;40(10):3080-8. PMID:11258922<ref>PMID:11258922</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1ic6" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Proteinase 3D structures|Proteinase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Parengyodontium album]] | |||
[[Category: Betzel C]] | |||
[[Category: Eschenburg S]] | |||
[[Category: Gourinath S]] | |||
[[Category: Kaur P]] | |||
[[Category: Kumar P]] | |||
[[Category: Perbandt M]] | |||
[[Category: Singh TP]] | |||
Latest revision as of 11:31, 6 November 2024
STRUCTURE OF A SERINE PROTEASE PROTEINASE K FROM TRITIRACHIUM ALBUM LIMBER AT 0.98 A RESOLUTIONSTRUCTURE OF A SERINE PROTEASE PROTEINASE K FROM TRITIRACHIUM ALBUM LIMBER AT 0.98 A RESOLUTION
Structural highlights
FunctionPRTK_PARAQ Hydrolyzes keratin at aromatic and hydrophobic residues. 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 PubMedX-ray diffraction data at atomic resolution to 0.98 A with 136 380 observed unique reflections were collected using a high quality proteinase K crystals grown under microgravity conditions and cryocooled. The structure has been refined anisotropically with REFMAC and SHELX-97 with R-factors of 11.4 and 12.8%, and R(free)-factors of 12.4 and 13.5%, respectively. The refined model coordinates have an overall rms shifts of 0.23 A relative to the same structure determined at room temperature at 1.5 A resolution. Several regions of the main chain and the side chains, which were not observed earlier have been seen more clearly. For example, amino acid 207, which was reported earlier as Ser has been clearly identified as Asp. Furthermore, side-chain disorders of 8 of 279 residues in the polypeptide have been identified. Hydrogen atoms appear as significant peaks in the F(o) - F(c) difference electron density map accounting for an estimated 46% of all hydrogen atoms at 2sigma level. Furthermore, the carbon, nitrogen, and oxygen atoms can be differentiated clearly in the electron density maps. Hydrogen bonds are clearly identified in the serine protease catalytic triad (Ser-His-Asp). Furthermore, electron density is observed for an unusual, short hydrogen bond between aspartic acid and histidine in the catalytic triad. The short hydrogen bond, designated "catalytic hydrogen bond", occurs as part of an elaborate hydrogen bond network, involving Asp of the catalytic triad. Though unusual, these features seem to be conserved in other serine proteases. Finally there are clear electron density peaks for the hydrogen atoms associated with the Ogamma of Ser 224 and Ndelta1 of His 69. Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 A resolution.,Betzel C, Gourinath S, Kumar P, Kaur P, Perbandt M, Eschenburg S, Singh TP Biochemistry. 2001 Mar 13;40(10):3080-8. PMID:11258922[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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