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.


3hdi

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:20, 6 September 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3hdi.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of Bacillus halodurans metallo peptidase==
-
The line below this paragraph, containing "STRUCTURE_3hdi", creates the "Structure Box" on the page.
+
<StructureSection load='3hdi' size='340' side='right'caption='[[3hdi]], [[Resolution|resolution]] 2.70&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'>[[3hdi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HDI 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]] 2.7&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_3hdi| PDB=3hdi | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hdi OCA], [https://pdbe.org/3hdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hdi RCSB], [https://www.ebi.ac.uk/pdbsum/3hdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hdi ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q9KA85_HALH5 Q9KA85_HALH5]
 +
== 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/hd/3hdi_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=3hdi ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The M16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a "clam-shell" surrounding the active site. The M16A and M16C subfamilies form one class ("peptidasomes"): they degrade 30-70 residue peptides, and adopt both open and closed conformations. The eukaryotic M16B subfamily forms a second class ("processing proteases"): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. Here, we report the solution and crystal structures of a prokaryotic M16B peptidase, and demonstrate that it has features of both classes: thus, it forms stable "open" homodimers in solution that resemble the processing proteases; but the clam-shell closes upon binding substrate, a feature of the M16A/C peptidasomes. Moreover, clam-shell closure is required for proteolytic activity. We predict that other prokaryotic M16B family members will form dimeric peptidasomes, and propose a model for the evolution of the M16 family.
-
===Crystal structure of Bacillus halodurans metallo peptidase===
+
Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case.,Aleshin AE, Gramatikova S, Hura GL, Bobkov A, Strongin AY, Stec B, Tainer JA, Liddington RC, Smith JW Structure. 2009 Nov 11;17(11):1465-75. PMID:19913481<ref>PMID:19913481</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_19913481}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3hdi" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 19913481 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_19913481}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Alkalihalobacillus halodurans C-125]]
-
3HDI is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HDI OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Aleshin A]]
-
==Reference==
+
[[Category: Gramatikova S]]
-
<ref group="xtra">PMID:19913481</ref><references group="xtra"/>
+
[[Category: Liddington RC]]
-
[[Category: Bacteria]]
+
[[Category: Smith JW]]
-
[[Category: Aleshin, A.]]
+
[[Category: Stec B]]
-
[[Category: Gramatikova, S.]]
+
[[Category: Strongin AY]]
-
[[Category: Liddington, R C.]]
+
-
[[Category: Smith, J W.]]
+
-
[[Category: Stec, B.]]
+
-
[[Category: Strongin, A Y.]]
+
-
[[Category: Cage structure]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: M16b peptidase]]
+
-
[[Category: Metallopeptidase]]
+
-
[[Category: Peptidasome]]
+
-
[[Category: Protease]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 9 15:05:35 2009''
+

Current revision

Crystal structure of Bacillus halodurans metallo peptidase

PDB ID 3hdi

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3hdi"
Personal tools