2tec: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2tec.jpg|left|200px]]


{{Structure
==MOLECULAR DYNAMICS REFINEMENT OF A THERMITASE-EGLIN-C COMPLEX AT 1.98 ANGSTROMS RESOLUTION AND COMPARISON OF TWO CRYSTAL FORMS THAT DIFFER IN CALCIUM CONTENT==
|PDB= 2tec |SIZE=350|CAPTION= <scene name='initialview01'>2tec</scene>, resolution 1.98&Aring;
<StructureSection load='2tec' size='340' side='right'caption='[[2tec]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene>
<table><tr><td colspan='2'>[[2tec]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Poecilobdella_manillensis Poecilobdella manillensis] and [https://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2TEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2TEC FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Thermitase Thermitase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.66 3.4.21.66]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
|GENE=  
<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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2tec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2tec OCA], [https://pdbe.org/2tec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2tec RCSB], [https://www.ebi.ac.uk/pdbsum/2tec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2tec ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ICIC_HIRME ICIC_HIRME] Inhibits both elastase and cathepsin G.
== 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/te/2tec_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=2tec ConSurf].
<div style="clear:both"></div>


'''MOLECULAR DYNAMICS REFINEMENT OF A THERMITASE-EGLIN-C COMPLEX AT 1.98 ANGSTROMS RESOLUTION AND COMPARISON OF TWO CRYSTAL FORMS THAT DIFFER IN CALCIUM CONTENT'''
==See Also==
 
*[[Eglin|Eglin]]
 
__TOC__
==Overview==
</StructureSection>
The crystal structure of the complex of thermitase with eglin-c in crystal form II, obtained in the presence of 5 mM-CaCl2, has been determined at 1.98 A resolution. The structure was solved by a molecular replacement method, then molecular dynamics crystallographic refinement was started using the thermitase-eglin-c structure as determined for crystal form I. A ten degrees rigid body misplacement of the core of eglin-c was corrected by the molecular dynamics crystallographic refinement without any need for manual rebuilding on a graphics system. A final crystallographic R-factor of 16.5% was obtained for crystal form II. The comparison of the complexes of thermitase with eglin-c in the two crystal forms shows that the eglin-c cores are differently oriented with respect to the protease. The inhibiting loop of eglin binds in a similar way to thermitase as to subtilisin Carlsberg. A tryptophanyl residue at the S4 site explains the preference of thermitase for aromatic residues of the substrate at the P4 site. The difference in the P1 binding pocket, asparagine in thermitase instead of glycine in subtilisin Carlsberg, does not change the binding of eglin-c. The preference for an arginyl residue at the P1 site of thermitase can be explained by the hydrogen bonding with Asn170 in thermitase. Three ion-binding sites of thermitase have been identified. The strong and weak calcium-binding sites resemble the equivalent sites of subtilisin Carlsberg and subtilisin BPN', though there are important amino acid differences at the calcium-binding sites. The medium-strength calcium-binding site of thermitase is observed in the subtilisin family for the first time. The calcium is bound to residues from the loop 57 to 66. A difference in chelation is observed at this site between the two crystal forms of thermitase, which differ in calcium concentration. Additional electron density is observed near Asp60 in crystal form II, which has more calcium bound than form I. This density is possibly due to a water molecule ligating the calcium ion or the result of Asp60 assuming two significantly different conformations.
[[Category: Large Structures]]
 
[[Category: Poecilobdella manillensis]]
==About this Structure==
2TEC is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Hirudinaria_manillensis Hirudinaria manillensis] and [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2TEC OCA].
 
==Reference==
Molecular dynamics refinement of a thermitase-eglin-c complex at 1.98 A resolution and comparison of two crystal forms that differ in calcium content., Gros P, Betzel C, Dauter Z, Wilson KS, Hol WG, J Mol Biol. 1989 Nov 20;210(2):347-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2689655 2689655]
[[Category: Hirudinaria manillensis]]
[[Category: Protein complex]]
[[Category: Thermitase]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Betzel, C.]]
[[Category: Betzel C]]
[[Category: Dauter, Z.]]
[[Category: Dauter Z]]
[[Category: Gros, P.]]
[[Category: Gros P]]
[[Category: Hol, W G.J.]]
[[Category: Hol WGJ]]
[[Category: Wilson, K S.]]
[[Category: Wilson KS]]
[[Category: CA]]
[[Category: complex(serine proteinase-inhibitor)]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:39:00 2008''

Latest revision as of 12:24, 21 February 2024

MOLECULAR DYNAMICS REFINEMENT OF A THERMITASE-EGLIN-C COMPLEX AT 1.98 ANGSTROMS RESOLUTION AND COMPARISON OF TWO CRYSTAL FORMS THAT DIFFER IN CALCIUM CONTENTMOLECULAR DYNAMICS REFINEMENT OF A THERMITASE-EGLIN-C COMPLEX AT 1.98 ANGSTROMS RESOLUTION AND COMPARISON OF TWO CRYSTAL FORMS THAT DIFFER IN CALCIUM CONTENT

Structural highlights

2tec is a 2 chain structure with sequence from Poecilobdella manillensis and Thermoactinomyces vulgaris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.98Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ICIC_HIRME Inhibits both elastase and cathepsin G.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2tec, resolution 1.98Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2tec&oldid=4063309"