1dc6: Difference between revisions

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STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES.

OverviewOverview

The crystal structures of gyceraldehyde 3-phosphate dehydrogenase (GAPDH) from Escherichia coli have been determined in three different enzymatic states, NAD(+)-free, NAD(+)-bound, and hemiacetal intermediate. The NAD(+)-free structure reported here has been determined from monoclinic and tetragonal crystal forms. The conformational changes in GAPDH induced by cofactor binding are limited to the residues that bind the adenine moiety of NAD(+). Glyceraldehyde 3-phosphate (GAP), the substrate of GAPDH, binds to the enzyme with its C3 phosphate in a hydrophilic pocket, called the "new P(i)" site, which is different from the originally proposed binding site for inorganic phosphate. This observed location of the C3 phosphate is consistent with the flip-flop model proposed for the enzyme mechanism [Skarzynski, T., Moody, P. C., and Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187]. Via incorporation of the new P(i) site in this model, it is now proposed that the C3 phosphate of GAP initially binds at the new P(i) site and then flips to the P(s) site before hydride transfer. A superposition of NAD(+)-bound and hemiacetal intermediate structures reveals an interaction between the hydroxyl oxygen at the hemiacetal C1 of GAP and the nicotinamide ring. This finding suggests that the cofactor NAD(+) may stabilize the transition state oxyanion of the hemiacetal intermediate in support of the flip-flop model for GAP binding.

About this StructureAbout this Structure

1DC6 is a Single protein structure of sequence from Escherichia coli with as ligand. Active as Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), with EC number 1.2.1.12 Full crystallographic information is available from OCA.

ReferenceReference

Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes., Yun M, Park CG, Kim JY, Park HW, Biochemistry. 2000 Sep 5;39(35):10702-10. PMID:10978154

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-[[Image:1dc6.jpg|left|200px]]<br /><applet load="1dc6" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1dc6.jpg|left|200px]]<br /><applet load="1dc6" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1dc6, resolution 2.0&Aring;" />
 '''STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES.'''<br />
 ==Overview==
-The crystal structures of gyceraldehyde 3-phosphate dehydrogenase (GAPDH), from Escherichia coli have been determined in three different enzymatic, states, NAD(+)-free, NAD(+)-bound, and hemiacetal intermediate. The, NAD(+)-free structure reported here has been determined from monoclinic, and tetragonal crystal forms. The conformational changes in GAPDH induced, by cofactor binding are limited to the residues that bind the adenine, moiety of NAD(+). Glyceraldehyde 3-phosphate (GAP), the substrate of, GAPDH, binds to the enzyme with its C3 phosphate in a hydrophilic pocket, called the "new P(i)" site, which is different from the originally, proposed binding site for inorganic phosphate. This observed location of, the C3 phosphate is consistent with the flip-flop model proposed for the, enzyme mechanism [Skarzynski, T., Moody, P. C., and Wonacott, A. J. (1987), J. Mol. Biol. 193, 171-187]. Via incorporation of the new P(i) site in, this model, it is now proposed that the C3 phosphate of GAP initially, binds at the new P(i) site and then flips to the P(s) site before hydride, transfer. A superposition of NAD(+)-bound and hemiacetal intermediate, structures reveals an interaction between the hydroxyl oxygen at the, hemiacetal C1 of GAP and the nicotinamide ring. This finding suggests that, the cofactor NAD(+) may stabilize the transition state oxyanion of the, hemiacetal intermediate in support of the flip-flop model for GAP binding.
+The crystal structures of gyceraldehyde 3-phosphate dehydrogenase (GAPDH) from Escherichia coli have been determined in three different enzymatic states, NAD(+)-free, NAD(+)-bound, and hemiacetal intermediate. The NAD(+)-free structure reported here has been determined from monoclinic and tetragonal crystal forms. The conformational changes in GAPDH induced by cofactor binding are limited to the residues that bind the adenine moiety of NAD(+). Glyceraldehyde 3-phosphate (GAP), the substrate of GAPDH, binds to the enzyme with its C3 phosphate in a hydrophilic pocket, called the "new P(i)" site, which is different from the originally proposed binding site for inorganic phosphate. This observed location of the C3 phosphate is consistent with the flip-flop model proposed for the enzyme mechanism [Skarzynski, T., Moody, P. C., and Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187]. Via incorporation of the new P(i) site in this model, it is now proposed that the C3 phosphate of GAP initially binds at the new P(i) site and then flips to the P(s) site before hydride transfer. A superposition of NAD(+)-bound and hemiacetal intermediate structures reveals an interaction between the hydroxyl oxygen at the hemiacetal C1 of GAP and the nicotinamide ring. This finding suggests that the cofactor NAD(+) may stabilize the transition state oxyanion of the hemiacetal intermediate in support of the flip-flop model for GAP binding.
 ==About this Structure==
-DC6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with NAD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DC6 OCA].
+DC6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC6 OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)]]
 [[Category: Single protein]]
-[[Category: Kim, J.Y.]]
+[[Category: Kim, J Y.]]
-[[Category: Park, C.G.]]
+[[Category: Park, C G.]]
-[[Category: Park, H.W.]]
+[[Category: Park, H W.]]
 [[Category: Yun, M.]]
 [[Category: NAD]]
@@ Line 23: / Line 23: @@
 [[Category: structure]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:09:38 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:15:10 2008''