1pdz: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1pdz.jpg|left|200px]] | [[Image:1pdz.jpg|left|200px]] | ||
'''X-RAY STRUCTURE AND CATALYTIC MECHANISM OF LOBSTER ENOLASE''' | {{Structure | ||
|PDB= 1pdz |SIZE=350|CAPTION= <scene name='initialview01'>1pdz</scene>, resolution 2.2Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> and <scene name='pdbligand=ACE:ACETYL GROUP'>ACE</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Phosphopyruvate_hydratase Phosphopyruvate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.11 4.2.1.11] | |||
|GENE= | |||
}} | |||
'''X-RAY STRUCTURE AND CATALYTIC MECHANISM OF LOBSTER ENOLASE''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
1PDZ is a [ | 1PDZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homarus_gammarus Homarus gammarus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDZ OCA]. | ||
==Reference== | ==Reference== | ||
X-ray structure and catalytic mechanism of lobster enolase., Duquerroy S, Camus C, Janin J, Biochemistry. 1995 Oct 3;34(39):12513-23. PMID:[http:// | X-ray structure and catalytic mechanism of lobster enolase., Duquerroy S, Camus C, Janin J, Biochemistry. 1995 Oct 3;34(39):12513-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7547999 7547999] | ||
[[Category: Homarus gammarus]] | [[Category: Homarus gammarus]] | ||
[[Category: Phosphopyruvate hydratase]] | [[Category: Phosphopyruvate hydratase]] | ||
| Line 23: | Line 32: | ||
[[Category: lyase (carbon-oxygen)]] | [[Category: lyase (carbon-oxygen)]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:23:11 2008'' | ||
Revision as of 14:23, 20 March 2008
| |||||||
| , resolution 2.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Activity: | Phosphopyruvate hydratase, with EC number 4.2.1.11 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
X-RAY STRUCTURE AND CATALYTIC MECHANISM OF LOBSTER ENOLASE
OverviewOverview
Enolase prepared from lobster tail muscle yielded trigonal crystals with one 47 kDa subunit per asymmetric unit. X-ray data were collected on the apoenzyme at 2.4 A resolution and on a complex with Mn2+ and the inhibitor phosphoglycolate at 2.2 A resolution. The corresponding cDNA was amplified from a library of lobster muscle cDNA, and a sequence corresponding to residues 27-398 was determined. It is highly homologous to other enolases, including yeast enolase for which an X-ray structure is available. Yeast enolase was used as a starting point for crystallographic refinement, which led to models of lobster enolase having R-factors below 22% and good stereochemistry. These models are very similar to yeast enolase; they have the same fold with a beta 3 alpha 4 N-terminal domain followed by an atypical alpha/beta barrel. Lobster apoenolase and the ternary complex differ only in the position of three mobile loops. In the complex, a single Mn2+ ion is seen ligated to three carboxylates and three water molecules. Phosphoglycolate binds near, but not directly to, the metal. His 157, which belongs to one of the mobile loops, is in contact with the C2 atom of the ligand. A water molecule hydrogen-bonds to the carboxylate of the ligand and to those of Glu 166 and Glu 209. We suggest that His 157 is the base that abstracts the C2H proton, whereas the water molecule is part of a proton relay system keeping the substrate in the carboxylic acid form where the pKa of the C2H group is low enough for proton transfer to His 157. The resulting catalytic mechanism is different from those proposed on the basis of the yeast enzyme X-ray structures, but it fits with earlier biochemical and spectroscopic data.
About this StructureAbout this Structure
1PDZ is a Single protein structure of sequence from Homarus gammarus. Full crystallographic information is available from OCA.
ReferenceReference
X-ray structure and catalytic mechanism of lobster enolase., Duquerroy S, Camus C, Janin J, Biochemistry. 1995 Oct 3;34(39):12513-23. PMID:7547999
Page seeded by OCA on Thu Mar 20 13:23:11 2008