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.

2z2z

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:12, 10 November 2021

Crystal structure of unautoprocessed form of Tk-subtilisin soaked by 10mM CaCl2

Structural highlights

2z2z is a 1 chain structure with sequence from Pyrococcus kodakaraensis (strain kod1). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2z2x, 2z2y, 2z30
Activity:	Subtilisin, with EC number 3.4.21.62
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TKSU_THEKO] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position.

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 PubMed

Subtilisin from the hyperthermophilic archaeon Thermococcus kodakaraensis (Tk-subtilisin) is matured from Pro-Tk-subtilisin upon autoprocessing and degradation of the propeptide. The crystal structures of the autoprocessed and mature forms of Tk-subtilisin were determined at 1.89 A and 1.70 A resolution, respectively. Comparison of these structures with that of unautoprocessed Pro-Tk-subtilisin indicates that the structure of Tk-subtilisin is not seriously changed during maturation. However, one unique Ca(2+)-binding site (Ca-7) is identified in these structures. In addition, the N-terminal region of the mature domain (Gly70-Pro82), which binds tightly to the main body in the unautoprocessed form, is disordered and mostly truncated in the autoprocessed and mature forms, respectively. Interestingly, this site is formed also in the unautoprocessed form when its crystals are soaked with 10 mM CaCl(2), as revealed by the 1.87 A structure. Along with the formation of this site, the N-terminal region (Leu75-Thr80) is disordered, with the scissile peptide bond contacting with the active site. These results indicate that the calcium ion binds weakly to the Ca-7 site in the unautoprocessed form, but is trapped upon autoprocessing. We propose that the Ca-7 site is required to promote the autoprocessing reaction by stabilizing the autoprocessed form, in which the new N terminus of the mature domain is structurally disordered. Furthermore, the crystal structure of the Tk-propeptide:S324A-subtilisin complex, which was formed by the addition of separately expressed proteins, was determined at 1.65 A resolution. This structure is virtually identical with that of the autoprocessed form, indicating that the interaction between the two domains is highly intensive and specific.

Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation.,Tanaka S, Matsumura H, Koga Y, Takano K, Kanaya S J Mol Biol. 2007 Sep 28;372(4):1055-69. Epub 2007 Jul 26. PMID:17706669^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tanaka S, Matsumura H, Koga Y, Takano K, Kanaya S. Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation. J Mol Biol. 2007 Sep 28;372(4):1055-69. Epub 2007 Jul 26. PMID:17706669 doi:http://dx.doi.org/10.1016/j.jmb.2007.07.027

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2z2z"

@@ Line 3: / Line 3: @@
 <StructureSection load='2z2z' size='340' side='right'caption='[[2z2z]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2z2z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2Z2Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2z2z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z2Z FirstGlance]. <br>
 </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></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2z2x|2z2x]], [[2z2y|2z2y]], [[2z30|2z30]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2z2x|2z2x]], [[2z2y|2z2y]], [[2z30|2z30]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2z2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2z OCA], [http://pdbe.org/2z2z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z2z RCSB], [http://www.ebi.ac.uk/pdbsum/2z2z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z2z ProSAT]</span></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=2z2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2z OCA], [https://pdbe.org/2z2z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z2z RCSB], [https://www.ebi.ac.uk/pdbsum/2z2z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z2z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO]] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position.
+[[https://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO]] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

2z2z

From Proteopedia

Revision as of 07:12, 10 November 2021

Crystal structure of unautoprocessed form of Tk-subtilisin soaked by 10mM CaCl2

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox