3grs: Difference between revisions
New page: left|200px<br /> <applet load="3grs" size="450" color="white" frame="true" align="right" spinBox="true" caption="3grs, resolution 1.54Å" /> '''REFINED STRUCTURE O... |
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[[Image:3grs.gif|left|200px]]<br /> | [[Image:3grs.gif|left|200px]]<br /><applet load="3grs" size="350" color="white" frame="true" align="right" spinBox="true" | ||
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caption="3grs, resolution 1.54Å" /> | caption="3grs, resolution 1.54Å" /> | ||
'''REFINED STRUCTURE OF GLUTATHIONE REDUCTASE AT 1.54 ANGSTROMS RESOLUTION'''<br /> | '''REFINED STRUCTURE OF GLUTATHIONE REDUCTASE AT 1.54 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
The crystal structure of human glutathione reductase has been established | The crystal structure of human glutathione reductase has been established at 1.54 A resolution using a restrained least-squares refinement method. Based on 77,690 independent reflections of better than 10 A resolution, a final R-factor of 18.6% was obtained with a model obeying standard geometry within 0.025 A in bond lengths and 2.4 degrees in bond angles. The final 2Fo-Fc electron density map allows for the distinction of carbon, nitrogen and oxygen atoms with temperature factors below about 25 A2. Apart from 461 amino acid residues and the prosthetic group FAD, the model contains 524 solvent molecules, about 118 of which can be considered an integral part of the enzyme. The largest solvent cluster is at the dimer interface and contains 104 interconnected solvent molecules, part of which are organized in a warped sheet-like structure. The main-chain dihedral angles are well-concentrated in the allowed regions of the Ramachandran plot. The spread of dihedral angles in beta-pleated sheets is much larger than in alpha-helices and especially in alpha-helix cores, indicating the higher plasticity of beta-structures. The analysis revealed a large amount of 3(10)-helix. The side-chain conformations cluster at the staggered positions, and show well-defined preferences. Also, a mobility gradient is observed for side-chains. Non-polar and polar side-chains show average temperature factor increases per bond of 10% and 25%, respectively. A number of alternative conformations of internal side-chains, in particular serines and methionines, have been detected. The extended FAD molecule also shows a mobility gradient between the very rigid flavin (mean value of B) = 8.7 A2) and the more mobile adenine (mean value of B = 16.2 A2). The entire active center is particularly well ordered, with temperature factors around 10 A2. The dimer interface consists of a rigid contact area, which is well conserved in the Escherichia coli enzyme, and a flexible area that is not. Altogether, the buried surfaces at the crystal contacts are half as large as at the dimer interface, but less specific. The refined structure shows clearly that there are no buried cations compensating the charge of the pyrophosphate moiety of FAD. The flavin deviates slightly from standard geometry, which is possibly caused by the polypeptide environment. In contrast to an earlier interpretation, atom N5 of the flavin can accommodate a proton, and it is conceivable that this proton proceeds to the redox-active disulfide.(ABSTRACT TRUNCATED AT 400 WORDS) | ||
==Disease== | ==Disease== | ||
Known | Known diseases associated with this structure: Hemolytic anemia due to glutathione reductase deficiency OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=138300 138300]], Mental retardation, autosomal recessive, 6 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=138244 138244]] | ||
==About this Structure== | ==About this Structure== | ||
3GRS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with PO4 and FAD as [http://en.wikipedia.org/wiki/ligands ligands]. This structure | 3GRS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=FAD:'>FAD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entries 2GRS and 1GRS. Active as [http://en.wikipedia.org/wiki/Glutathione-disulfide_reductase Glutathione-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.7 1.8.1.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRS OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Karplus, P | [[Category: Karplus, P A.]] | ||
[[Category: Schulz, G | [[Category: Schulz, G E.]] | ||
[[Category: FAD]] | [[Category: FAD]] | ||
[[Category: PO4]] | [[Category: PO4]] | ||
[[Category: oxidoreductase (flavoenzyme)]] | [[Category: oxidoreductase (flavoenzyme)]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:09:34 2008'' | ||
Revision as of 20:09, 21 February 2008
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REFINED STRUCTURE OF GLUTATHIONE REDUCTASE AT 1.54 ANGSTROMS RESOLUTION
OverviewOverview
The crystal structure of human glutathione reductase has been established at 1.54 A resolution using a restrained least-squares refinement method. Based on 77,690 independent reflections of better than 10 A resolution, a final R-factor of 18.6% was obtained with a model obeying standard geometry within 0.025 A in bond lengths and 2.4 degrees in bond angles. The final 2Fo-Fc electron density map allows for the distinction of carbon, nitrogen and oxygen atoms with temperature factors below about 25 A2. Apart from 461 amino acid residues and the prosthetic group FAD, the model contains 524 solvent molecules, about 118 of which can be considered an integral part of the enzyme. The largest solvent cluster is at the dimer interface and contains 104 interconnected solvent molecules, part of which are organized in a warped sheet-like structure. The main-chain dihedral angles are well-concentrated in the allowed regions of the Ramachandran plot. The spread of dihedral angles in beta-pleated sheets is much larger than in alpha-helices and especially in alpha-helix cores, indicating the higher plasticity of beta-structures. The analysis revealed a large amount of 3(10)-helix. The side-chain conformations cluster at the staggered positions, and show well-defined preferences. Also, a mobility gradient is observed for side-chains. Non-polar and polar side-chains show average temperature factor increases per bond of 10% and 25%, respectively. A number of alternative conformations of internal side-chains, in particular serines and methionines, have been detected. The extended FAD molecule also shows a mobility gradient between the very rigid flavin (mean value of B) = 8.7 A2) and the more mobile adenine (mean value of B = 16.2 A2). The entire active center is particularly well ordered, with temperature factors around 10 A2. The dimer interface consists of a rigid contact area, which is well conserved in the Escherichia coli enzyme, and a flexible area that is not. Altogether, the buried surfaces at the crystal contacts are half as large as at the dimer interface, but less specific. The refined structure shows clearly that there are no buried cations compensating the charge of the pyrophosphate moiety of FAD. The flavin deviates slightly from standard geometry, which is possibly caused by the polypeptide environment. In contrast to an earlier interpretation, atom N5 of the flavin can accommodate a proton, and it is conceivable that this proton proceeds to the redox-active disulfide.(ABSTRACT TRUNCATED AT 400 WORDS)
DiseaseDisease
Known diseases associated with this structure: Hemolytic anemia due to glutathione reductase deficiency OMIM:[138300], Mental retardation, autosomal recessive, 6 OMIM:[138244]
About this StructureAbout this Structure
3GRS is a Single protein structure of sequence from Homo sapiens with and as ligands. This structure supersedes the now removed PDB entries 2GRS and 1GRS. Active as Glutathione-disulfide reductase, with EC number 1.8.1.7 Full crystallographic information is available from OCA.
ReferenceReference
Refined structure of glutathione reductase at 1.54 A resolution., Karplus PA, Schulz GE, J Mol Biol. 1987 Jun 5;195(3):701-29. PMID:3656429
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