1srd
From Proteopedia
(New page: 200px<br /><applet load="1srd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1srd, resolution 2.0Å" /> '''THREE-DIMENSIONAL STR...) |
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| - | [[Image:1srd.jpg|left|200px]]<br /><applet load="1srd" size=" | + | [[Image:1srd.jpg|left|200px]]<br /><applet load="1srd" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1srd, resolution 2.0Å" /> | caption="1srd, resolution 2.0Å" /> | ||
'''THREE-DIMENSIONAL STRUCTURE OF CU,ZN-SUPEROXIDE DISMUTASE FROM SPINACH AT 2.0 ANGSTROMS RESOLUTION'''<br /> | '''THREE-DIMENSIONAL STRUCTURE OF CU,ZN-SUPEROXIDE DISMUTASE FROM SPINACH AT 2.0 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The three-dimensional structure of Cu,Zn-superoxide dismutase from spinach | + | The three-dimensional structure of Cu,Zn-superoxide dismutase from spinach leaves has been determined by X-ray crystal structure analysis. The atomic coordinates were refined at 2.0 A resolution using the Hendrickson and Konnert program for stereochemically restrained refinement against structure factors, which allowed the use of non-crystallographic symmetry. The crystallographic residual error for the refined model was 24.9%, with a root mean square deviation of 0.03 A from the ideal bond length and an average atomic temperature factor of 9.6 A. A dimeric molecule of the enzyme is comprised of two identical subunits related by a non-crystallographic 2-fold axis. Each subunit of 154 amino acid residues is composed primarily of eight anti-parallel beta-strands that form a flattened cylinder, plus three external loops. The main-chain hydrogen bonds primarily link the beta-strands. The overall structure of this enzyme is quite similar to that of the bovine dismutase except for some parts. The single disulfide bridge (Cys57-Cys146) and the salt bridge (Arg79-Asp101) may stabilize the loop regions of the structure. The Cu2+ and Zn2+ ions in the active site lie 6.1 A apart at the bottom of the long channel. The Cu2+ ligands (ND1 of His-46, and NE2 of His-48, -63, and -120) show an uneven tetrahedral distortion from a square plane. The Zn2+ ligands (ND1 of His-63, -71, and -80 and OD1 of Asp-83) show an almost tetrahedral geometry. The imidazole ring of His-63 forms a bridge between the Cu2+ and Zn2+ ions.(ABSTRACT TRUNCATED AT 250 WORDS) |
==About this Structure== | ==About this Structure== | ||
| - | 1SRD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea] with CU and ZN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] Full crystallographic information is available from [http:// | + | 1SRD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea] with <scene name='pdbligand=CU:'>CU</scene> and <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. |
==Reference== | ==Reference== | ||
| - | Three-dimensional structure of Cu,Zn-superoxide dismutase from spinach at 2.0 A resolution., Kitagawa Y, Tanaka N, Hata Y, Kusunoki M, Lee GP, Katsube Y, Asada K, Aibara S, Morita Y, J Biochem | + | Three-dimensional structure of Cu,Zn-superoxide dismutase from spinach at 2.0 A resolution., Kitagawa Y, Tanaka N, Hata Y, Kusunoki M, Lee GP, Katsube Y, Asada K, Aibara S, Morita Y, J Biochem. 1991 Mar;109(3):477-85. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1880134 1880134] |
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Spinacia oleracea]] | [[Category: Spinacia oleracea]] | ||
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[[Category: oxidoreductase(superoxide acceptor)]] | [[Category: oxidoreductase(superoxide acceptor)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:04:29 2008'' |
Revision as of 13:04, 21 February 2008
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THREE-DIMENSIONAL STRUCTURE OF CU,ZN-SUPEROXIDE DISMUTASE FROM SPINACH AT 2.0 ANGSTROMS RESOLUTION
Overview
The three-dimensional structure of Cu,Zn-superoxide dismutase from spinach leaves has been determined by X-ray crystal structure analysis. The atomic coordinates were refined at 2.0 A resolution using the Hendrickson and Konnert program for stereochemically restrained refinement against structure factors, which allowed the use of non-crystallographic symmetry. The crystallographic residual error for the refined model was 24.9%, with a root mean square deviation of 0.03 A from the ideal bond length and an average atomic temperature factor of 9.6 A. A dimeric molecule of the enzyme is comprised of two identical subunits related by a non-crystallographic 2-fold axis. Each subunit of 154 amino acid residues is composed primarily of eight anti-parallel beta-strands that form a flattened cylinder, plus three external loops. The main-chain hydrogen bonds primarily link the beta-strands. The overall structure of this enzyme is quite similar to that of the bovine dismutase except for some parts. The single disulfide bridge (Cys57-Cys146) and the salt bridge (Arg79-Asp101) may stabilize the loop regions of the structure. The Cu2+ and Zn2+ ions in the active site lie 6.1 A apart at the bottom of the long channel. The Cu2+ ligands (ND1 of His-46, and NE2 of His-48, -63, and -120) show an uneven tetrahedral distortion from a square plane. The Zn2+ ligands (ND1 of His-63, -71, and -80 and OD1 of Asp-83) show an almost tetrahedral geometry. The imidazole ring of His-63 forms a bridge between the Cu2+ and Zn2+ ions.(ABSTRACT TRUNCATED AT 250 WORDS)
About this Structure
1SRD is a Single protein structure of sequence from Spinacia oleracea with and as ligands. Active as Superoxide dismutase, with EC number 1.15.1.1 Full crystallographic information is available from OCA.
Reference
Three-dimensional structure of Cu,Zn-superoxide dismutase from spinach at 2.0 A resolution., Kitagawa Y, Tanaka N, Hata Y, Kusunoki M, Lee GP, Katsube Y, Asada K, Aibara S, Morita Y, J Biochem. 1991 Mar;109(3):477-85. PMID:1880134
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