1rdf: Difference between revisions

Revision as of 15:49, 21 February 2008

G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate

OverviewOverview

The haloacid dehalogenase (HAD) superfamily includes a variety of enzymes that catalyze the cleavage of substrate C-Cl, P-C, and P-OP bonds via nucleophilic substitution pathways. All members possess the alpha/beta core domain, and many also possess a small cap domain. The active site of the core domain is formed by four loops (corresponding to sequence motifs 1-4), which position substrate and cofactor-binding residues as well as the catalytic groups that mediate the "core" chemistry. The cap domain is responsible for the diversification of chemistry within the family. A tight beta-turn in the helix-loop-helix motif of the cap domain contains a stringently conserved Gly (within sequence motif 5), flanked by residues whose side chains contribute to the catalytic site formed at the domain-domain interface. To define the role of the conserved Gly in the structure and function of the cap domain loop of the HAD superfamily members phosphonoacetaldehyde hydrolase and beta-phosphoglucomutase, the Gly was mutated to Pro, Val, or Ala. The catalytic activity was severely reduced in each mutant. To examine the impact of Gly substitution on loop 5 conformation, the X-ray crystal structure of the Gly50Pro phosphonoacetaldehyde hydrolase mutant was determined. The altered backbone conformation at position 50 had a dramatic effect on the spatial disposition of the side chains of neighboring residues. Lys53, the Schiff Base forming lysine, had rotated out of the catalytic site and the side chain of Leu52 had moved to fill its place. On the basis of these studies, it was concluded that the flexibility afforded by the conserved Gly is critical to the function of loop 5 and that it is a marker by which the cap domain substrate specificity loop can be identified within the amino acid sequence of HAD family members.

About this StructureAbout this Structure

1RDF is a Single protein structure of sequence from Bacillus cereus with and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

Analysis of the substrate specificity loop of the HAD superfamily cap domain., Lahiri SD, Zhang G, Dai J, Dunaway-Mariano D, Allen KN, Biochemistry. 2004 Mar 16;43(10):2812-20. PMID:15005616

Page seeded by OCA on Thu Feb 21 14:49:40 2008

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OCA

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-[[Image:1rdf.gif|left|200px]]<br /><applet load="1rdf" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1rdf.gif|left|200px]]<br /><applet load="1rdf" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1rdf, resolution 2.80&Aring;" />
 '''G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate'''<br />
 ==Overview==
-The haloacid dehalogenase (HAD) superfamily includes a variety of enzymes, that catalyze the cleavage of substrate C-Cl, P-C, and P-OP bonds via, nucleophilic substitution pathways. All members possess the alpha/beta, core domain, and many also possess a small cap domain. The active site of, the core domain is formed by four loops (corresponding to sequence motifs, 1-4), which position substrate and cofactor-binding residues as well as, the catalytic groups that mediate the "core" chemistry. The cap domain is, responsible for the diversification of chemistry within the family. A, tight beta-turn in the helix-loop-helix motif of the cap domain contains a, stringently conserved Gly (within sequence motif 5), flanked by residues, whose side chains contribute to the catalytic site formed at the, domain-domain interface. To define the role of the conserved Gly in the, structure and function of the cap domain loop of the HAD superfamily, members phosphonoacetaldehyde hydrolase and beta-phosphoglucomutase, the, Gly was mutated to Pro, Val, or Ala. The catalytic activity was severely, reduced in each mutant. To examine the impact of Gly substitution on loop, 5 conformation, the X-ray crystal structure of the Gly50Pro, phosphonoacetaldehyde hydrolase mutant was determined. The altered, backbone conformation at position 50 had a dramatic effect on the spatial, disposition of the side chains of neighboring residues. Lys53, the Schiff, Base forming lysine, had rotated out of the catalytic site and the side, chain of Leu52 had moved to fill its place. On the basis of these studies, it was concluded that the flexibility afforded by the conserved Gly is, critical to the function of loop 5 and that it is a marker by which the, cap domain substrate specificity loop can be identified within the amino, acid sequence of HAD family members.
+The haloacid dehalogenase (HAD) superfamily includes a variety of enzymes that catalyze the cleavage of substrate C-Cl, P-C, and P-OP bonds via nucleophilic substitution pathways. All members possess the alpha/beta core domain, and many also possess a small cap domain. The active site of the core domain is formed by four loops (corresponding to sequence motifs 1-4), which position substrate and cofactor-binding residues as well as the catalytic groups that mediate the "core" chemistry. The cap domain is responsible for the diversification of chemistry within the family. A tight beta-turn in the helix-loop-helix motif of the cap domain contains a stringently conserved Gly (within sequence motif 5), flanked by residues whose side chains contribute to the catalytic site formed at the domain-domain interface. To define the role of the conserved Gly in the structure and function of the cap domain loop of the HAD superfamily members phosphonoacetaldehyde hydrolase and beta-phosphoglucomutase, the Gly was mutated to Pro, Val, or Ala. The catalytic activity was severely reduced in each mutant. To examine the impact of Gly substitution on loop 5 conformation, the X-ray crystal structure of the Gly50Pro phosphonoacetaldehyde hydrolase mutant was determined. The altered backbone conformation at position 50 had a dramatic effect on the spatial disposition of the side chains of neighboring residues. Lys53, the Schiff Base forming lysine, had rotated out of the catalytic site and the side chain of Leu52 had moved to fill its place. On the basis of these studies, it was concluded that the flexibility afforded by the conserved Gly is critical to the function of loop 5 and that it is a marker by which the cap domain substrate specificity loop can be identified within the amino acid sequence of HAD family members.
 ==About this Structure==
-RDF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus] with MG and ESA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RDF OCA].
+RDF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ESA:'>ESA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDF OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Bacillus cereus]]
 [[Category: Single protein]]
-[[Category: Allen, K.N.]]
+[[Category: Allen, K N.]]
 [[Category: Dunaway-Mariano, D.]]
-[[Category: Lahiri, S.D.]]
+[[Category: Lahiri, S D.]]
 [[Category: Zhang, G.]]
 [[Category: ESA]]
@@ Line 24: / Line 24: @@
 [[Category: specificity loop]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:29:26 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:49:40 2008''