1z8j

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:1z8j.gif|left|200px]]<br /><applet load="1z8j" size="350" color="white" frame="true" align="right" spinBox="true"
+
[[Image:1z8j.gif|left|200px]]
-
caption="1z8j, resolution 2.00&Aring;" />
+
 
-
'''Crystal structure of the thrombin mutant G193P bound to PPACK'''<br />
+
{{Structure
 +
|PDB= 1z8j |SIZE=350|CAPTION= <scene name='initialview01'>1z8j</scene>, resolution 2.00&Aring;
 +
|SITE=
 +
|LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
 +
|ACTIVITY= [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5]
 +
|GENE= F2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
 +
}}
 +
 
 +
'''Crystal structure of the thrombin mutant G193P bound to PPACK'''
 +
 
==Overview==
==Overview==
Line 10: Line 19:
==About this Structure==
==About this Structure==
-
1Z8J is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=NAG:'>NAG</scene>, <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z8J OCA].
+
1Z8J is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z8J OCA].
==Reference==
==Reference==
-
Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases., Bobofchak KM, Pineda AO, Mathews FS, Di Cera E, J Biol Chem. 2005 Jul 8;280(27):25644-50. Epub 2005 May 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15890651 15890651]
+
Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases., Bobofchak KM, Pineda AO, Mathews FS, Di Cera E, J Biol Chem. 2005 Jul 8;280(27):25644-50. Epub 2005 May 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15890651 15890651]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Protein complex]]
[[Category: Protein complex]]
Line 27: Line 36:
[[Category: serine protease]]
[[Category: serine protease]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:13:09 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:32:25 2008''

Revision as of 13:32, 20 March 2008

Image:1z8j.gif


PDB ID 1z8j

Drag the structure with the mouse to rotate
, resolution 2.00Å
Ligands: , and
Gene: F2 (Homo sapiens)
Activity: Thrombin, with EC number 3.4.21.5
Coordinates: save as pdb, mmCIF, xml



Crystal structure of the thrombin mutant G193P bound to PPACK


Contents

Overview

The oxyanion hole of serine proteases is formed by the backbone N atoms of the catalytic Ser-195 and Gly-193 and engages the backbone O atom of the P1 residue of substrate in an important H-bonding interaction. The energetic contribution of this interaction in the ground and transition states is presently unknown. Measurements of the individual rate constants defining the catalytic mechanism of substrate hydrolysis for wild-type thrombin and trypsin and their G193A and G193P mutants reveal that Gly-193 is required for optimal substrate binding and acylation. Crystal structures of the G193A and G193P mutants of thrombin bound to the active site inhibitor H-d-Phe-Pro-Arg-CH2Cl document the extent of perturbation induced by the replacement of Gly-193. The Ala mutant weakens the H-bonding interaction of the N atom of residue 193, whereas the Pro substitution abrogates it altogether with additional small shifts of the protein backbone. From the kinetic and structural data, we estimate that the H-bonding interaction in the oxyanion hole contributes a stabilization of the ground and transition states of > 1.5 kcal/mol but < 3.0 kcal/mol. These results shed light on a basic aspect of the enzyme-substrate interaction in the entire family of trypsin-like serine proteases.

Disease

Known diseases associated with this structure: Dysprothrombinemia OMIM:[176930], Hyperprothrombinemia OMIM:[176930], Hypoprothrombinemia OMIM:[176930]

About this Structure

1Z8J is a Protein complex structure of sequences from Homo sapiens. Full crystallographic information is available from OCA.

Reference

Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases., Bobofchak KM, Pineda AO, Mathews FS, Di Cera E, J Biol Chem. 2005 Jul 8;280(27):25644-50. Epub 2005 May 12. PMID:15890651

Page seeded by OCA on Thu Mar 20 15:32:25 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1z8j"
Personal tools