1dc6
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:1dc6.jpg|left|200px]] | + | [[Image:1dc6.jpg|left|200px]] |
| - | + | ||
| - | '''STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES.''' | + | {{Structure |
| + | |PDB= 1dc6 |SIZE=350|CAPTION= <scene name='initialview01'>1dc6</scene>, resolution 2.0Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> | ||
| + | |ACTIVITY= [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] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES.''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1DC6 is a [ | + | 1DC6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC6 OCA]. |
==Reference== | ==Reference== | ||
| - | 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:[http:// | + | 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:[http://www.ncbi.nlm.nih.gov/pubmed/10978154 10978154] |
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)]] | [[Category: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)]] | ||
| Line 23: | Line 32: | ||
[[Category: structure]] | [[Category: structure]] | ||
| - | ''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 10:36:09 2008'' |
Revision as of 08:36, 20 March 2008
| |||||||
| , resolution 2.0Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), with EC number 1.2.1.12 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES.
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.
About this Structure
1DC6 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Mar 20 10:36:09 2008
