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1wmd

From Proteopedia

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[[Image:1wmd.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of alkaline serine protease KP-43 from Bacillus sp. KSM-KP43 (1.30 angstrom, 100 K)==
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|PDB= 1wmd |SIZE=350|CAPTION= <scene name='initialview01'>1wmd</scene>, resolution 1.30&Aring;
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<StructureSection load='1wmd' size='340' side='right'caption='[[1wmd]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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<table><tr><td colspan='2'>[[1wmd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._KSM-KP43 Bacillus sp. KSM-KP43]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WMD FirstGlance]. <br>
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|ACTIVITY=
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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]] 1.3&#8491;</td></tr>
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|GENE=
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<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=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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}}
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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=1wmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wmd OCA], [https://pdbe.org/1wmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wmd RCSB], [https://www.ebi.ac.uk/pdbsum/1wmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wmd ProSAT]</span></td></tr>
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</table>
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'''Crystal Structure of alkaline serine protease KP-43 from Bacillus sp. KSM-KP43 (1.30 angstrom, 100 K)'''
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== Function ==
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[https://www.uniprot.org/uniprot/Q93UV9_9BACI Q93UV9_9BACI]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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The crystal structure of an oxidatively stable subtilisin-like alkaline serine protease, KP-43 from Bacillus sp. KSM-KP43, with a C-terminal extension domain, was determined by the multiple isomorphous replacements method with anomalous scattering. The native form was refined to a crystallographic R factor of 0.134 (Rfree of 0.169) at 1.30-A resolution. KP-43 consists of two domains, a subtilisin-like alpha/beta domain and a C-terminal jelly roll beta-barrel domain. The topological architecture of the molecule is similar to that of kexin and furin, which belong to the subtilisin-like proprotein convertases, whereas the amino acid sequence and the binding orientation of the C-terminal beta-barrel domain both differ in each case. Since the C-terminal domains of subtilisin-like proprotein convertases are essential for folding themselves, the domain of KP-43 is also thought to play such a role. KP-43 is known to be an oxidation-resistant protease among the general subtilisin-like proteases. To investigate how KP-43 resists oxidizing reagents, the structure of oxidized KP-43 was also determined and refined to a crystallographic R factor of 0.142 (Rfree of 0.212) at 1.73-A resolution. The structure analysis revealed that Met-256, adjacent to catalytic Ser-255, was oxidized similarly to an equivalent residue in subtilisin BPN'. Although KP-43, as well as proteinase K and subtilisin Carlsberg, lose their hydrolyzing activity against synthetic peptides after oxidation treatment, all of them retain 70-80% activity against proteinaceous substrates. These results, as well as the beta-casein digestion pattern analysis, have indicated that the oxidation of the methionine adjacent to the catalytic serine is not a dominant modification but might alter the substrate specificities.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wm/1wmd_consurf.spt"</scriptWhenChecked>
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1WMD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WMD OCA].
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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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==Reference==
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</jmolCheckbox>
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The crystal structure of an oxidatively stable subtilisin-like alkaline serine protease, KP-43, with a C-terminal beta-barrel domain., Nonaka T, Fujihashi M, Kita A, Saeki K, Ito S, Horikoshi K, Miki K, J Biol Chem. 2004 Nov 5;279(45):47344-51. Epub 2004 Sep 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15342641 15342641]
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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=1wmd ConSurf].
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[[Category: Bacteria]]
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<div style="clear:both"></div>
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[[Category: Single protein]]
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__TOC__
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[[Category: Fujihashi, M.]]
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</StructureSection>
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[[Category: Horikoshi, K.]]
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[[Category: Bacillus sp. KSM-KP43]]
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[[Category: Ito, S.]]
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[[Category: Large Structures]]
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[[Category: Kita, A.]]
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[[Category: Fujihashi M]]
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[[Category: Miki, K.]]
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[[Category: Horikoshi K]]
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[[Category: Nonaka, T.]]
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[[Category: Ito S]]
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[[Category: Saeki, K.]]
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[[Category: Kita A]]
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[[Category: CA]]
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[[Category: Miki K]]
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[[Category: DIO]]
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[[Category: Nonaka T]]
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[[Category: GOL]]
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[[Category: Saeki K]]
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[[Category: SO4]]
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[[Category: alpha-beta hydrolase fold]]
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[[Category: jelly-roll beta-barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:58:47 2008''
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Current revision

Crystal Structure of alkaline serine protease KP-43 from Bacillus sp. KSM-KP43 (1.30 angstrom, 100 K)

PDB ID 1wmd

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