1gpd
From Proteopedia
(New page: 200px<br /><applet load="1gpd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1gpd, resolution 2.9Å" /> '''STUDIES OF ASYMMETRY ...) |
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caption="1gpd, resolution 2.9Å" /> | caption="1gpd, resolution 2.9Å" /> | ||
'''STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE'''<br /> | '''STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | An improved electron density map of lobster | + | An improved electron density map of lobster holo-D-glyceraldehyde-3-phosphate dehydrogenase has been computed to 2.9 A resolution based on two heavy atom isomorphous derivatives. This has been averaged only over the Q molecular 2-fold axis, which is known to be exact in the human holoenzyme. The map showed possible asymmetry between the subunits in which the active centers are closely related across the R axis (that is, between the red and green or between the yellow and blue subunits). A difference map between the electron density of citrate and sulfate-soaked crystals gave further evidence for possible asymmetry. The major differences of electron density between R axis-related subunits appear around the active center and suggest the following interpretations. 1. The conformation of the adenine about the glycosidic bond is the more frequently observed anti with a C-2' endo conformation for the ribose ring in the red and yellow subunits, but is probably syn with a C-3' endo conformation in the green and blue subunits.2. The adenine ribose has its 3'-hydroxyl group hydrogen-bonded to a main chain carbonyl group in the red and yellow subunits but not in the green and blue subunits, as a consequence of the differing ribose conformations. 3. Cysteine-149 is more closely associated with histidine-176 in the green and blue subunits, and appears nearer the nicotinamide in the red and yellow subunits. |
==About this Structure== | ==About this Structure== | ||
| - | 1GPD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homarus_americanus Homarus americanus] with PO4, ACE and NAD as [http://en.wikipedia.org/wiki/ligands ligands]. 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:// | + | 1GPD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homarus_americanus Homarus americanus] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=ACE:'>ACE</scene> and <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1GPD OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Buehner, M.]] | [[Category: Buehner, M.]] | ||
| - | [[Category: Ford, G | + | [[Category: Ford, G C.]] |
[[Category: Moras, D.]] | [[Category: Moras, D.]] | ||
| - | [[Category: Olsen, K | + | [[Category: Olsen, K W.]] |
| - | [[Category: Rossmann, M | + | [[Category: Rossmann, M G.]] |
| - | [[Category: Sabesan, M | + | [[Category: Sabesan, M N.]] |
[[Category: ACE]] | [[Category: ACE]] | ||
[[Category: NAD]] | [[Category: NAD]] | ||
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[[Category: oxido-reductse(aldehyde/donr]] | [[Category: oxido-reductse(aldehyde/donr]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:52:33 2008'' |
Revision as of 10:52, 21 February 2008
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STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Overview
An improved electron density map of lobster holo-D-glyceraldehyde-3-phosphate dehydrogenase has been computed to 2.9 A resolution based on two heavy atom isomorphous derivatives. This has been averaged only over the Q molecular 2-fold axis, which is known to be exact in the human holoenzyme. The map showed possible asymmetry between the subunits in which the active centers are closely related across the R axis (that is, between the red and green or between the yellow and blue subunits). A difference map between the electron density of citrate and sulfate-soaked crystals gave further evidence for possible asymmetry. The major differences of electron density between R axis-related subunits appear around the active center and suggest the following interpretations. 1. The conformation of the adenine about the glycosidic bond is the more frequently observed anti with a C-2' endo conformation for the ribose ring in the red and yellow subunits, but is probably syn with a C-3' endo conformation in the green and blue subunits.2. The adenine ribose has its 3'-hydroxyl group hydrogen-bonded to a main chain carbonyl group in the red and yellow subunits but not in the green and blue subunits, as a consequence of the differing ribose conformations. 3. Cysteine-149 is more closely associated with histidine-176 in the green and blue subunits, and appears nearer the nicotinamide in the red and yellow subunits.
About this Structure
1GPD is a Single protein structure of sequence from Homarus americanus with , and as ligands. Active as Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), with EC number 1.2.1.12 Full crystallographic information is available from OCA.
Reference
Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase., Moras D, Olsen KW, Sabesan MN, Buehner M, Ford GC, Rossmann MG, J Biol Chem. 1975 Dec 10;250(23):9137-62. PMID:127793
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