1ldn: Difference between revisions

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Revision as of 13:29, 20 March 2008

File:1ldn.gif

, resolution 2.5Å

Ligands:

, and

Activity:

L-lactate dehydrogenase, with EC number 1.1.1.27

Coordinates:

save as pdb, mmCIF, xml

STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION

OverviewOverview

We report the refined structure of a ternary complex of an allosterically activated lactate dehydrogenase, including the important active site loop. Eightfold non-crystallographic symmetry averaging was utilized to improve the density maps. Interactions between the protein and bound coenzyme and oxamate are described in relation to other studies using site-specific mutagenesis. Fructose 1,6-bisphosphate (FruP2) is bound to the enzyme across one of the 2-fold axes of the tetramer, with the two phosphate moieties interacting with two anion binding sites, one on each of two subunits, across this interface. However, because FruP2 binds at this special site, yet does not possess an internal 2-fold symmetry axis, the ligand is statistically disordered and binds to each site in two different orientations. Binding of FruP2 to the tetramer is signalled to the active site principally through two interactions with His188 and Arg173. His188 is connected to His195 (which binds the carbonyl group of the substrate) and Arg173 is connected to Arg171 (the residue that binds the carboxylate group of the substrate).

About this StructureAbout this Structure

1LDN is a Single protein structure of sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA.

ReferenceReference

Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution., Wigley DB, Gamblin SJ, Turkenburg JP, Dodson EJ, Piontek K, Muirhead H, Holbrook JJ, J Mol Biol. 1992 Jan 5;223(1):317-35. PMID:1731077

Page seeded by OCA on Thu Mar 20 12:29:41 2008

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OCA

@@ Line 1: / Line 1: @@
-[[Image:1ldn.gif|left|200px]]<br /><applet load="1ldn" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1ldn.gif|left|200px]]
-caption="1ldn, resolution 2.5&Aring;" />
-'''STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION'''<br />
+ {{Structure
+|PDB= 1ldn |SIZE=350|CAPTION= <scene name='initialview01'>1ldn</scene>, resolution 2.5&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=FBP:FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=OXM:OXAMIC+ACID'>OXM</scene> and <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
+|ACTIVITY= [http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27]
+|GENE=
+}}
+'''STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-LDN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with <scene name='pdbligand=FBP:'>FBP</scene>, <scene name='pdbligand=OXM:'>OXM</scene> and <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDN OCA].
+LDN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDN OCA].
 ==Reference==
-Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution., Wigley DB, Gamblin SJ, Turkenburg JP, Dodson EJ, Piontek K, Muirhead H, Holbrook JJ, J Mol Biol. 1992 Jan 5;223(1):317-35. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1731077 1731077]
+Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution., Wigley DB, Gamblin SJ, Turkenburg JP, Dodson EJ, Piontek K, Muirhead H, Holbrook JJ, J Mol Biol. 1992 Jan 5;223(1):317-35. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1731077 1731077]
 [[Category: Geobacillus stearothermophilus]]
 [[Category: L-lactate dehydrogenase]]
@@ Line 26: / Line 35: @@
 [[Category: oxidoreductase(choh(d)-nad(a))]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:44:00 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:29:41 2008''