1gwf: Difference between revisions

Revision as of 13:54, 21 February 2008

COMPOUND II STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE

OverviewOverview

The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.

About this StructureAbout this Structure

1GWF is a Single protein structure of sequence from Micrococcus luteus with , , and as ligands. Active as Catalase, with EC number 1.11.1.6 Full crystallographic information is available from OCA.

ReferenceReference

The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex., Murshudov GN, Grebenko AI, Brannigan JA, Antson AA, Barynin VV, Dodson GG, Dauter Z, Wilson KS, Melik-Adamyan WR, Acta Crystallogr D Biol Crystallogr. 2002 Dec;58(Pt 12):1972-82. Epub 2002, Nov 23. PMID:12454454

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-[[Image:1gwf.jpg|left|200px]]<br /><applet load="1gwf" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1gwf.jpg|left|200px]]<br /><applet load="1gwf" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1gwf, resolution 1.96&Aring;" />
 '''COMPOUND II STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE'''<br />
 ==Overview==
-The crystal structure of the bacterial catalase from Micrococcus, lysodeikticus has been refined using the gene-derived sequence both at, 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution, with room-temperature data. The atomic resolution structure has been, refined with individual anisotropic atomic thermal parameters. This has, revealed the geometry of the haem and surrounding protein, including many, of the H atoms, with unprecedented accuracy and has characterized, functionally important hydrogen-bond interactions in the active site. The, positions of the H atoms are consistent with the enzymatic mechanism, previously suggested for beef liver catalase. The structure reveals that a, 25 A long channel leading to the haem is filled by partially occupied, water molecules, suggesting an inherent facile access to the active site., In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex, with NADPH at 1.83 A resolution have been determined. Comparison of, compound II and the resting state of the enzyme shows that the binding of, the O atom to the iron (bond length 1.87 A) is associated with increased, haem bending and is accompanied by a distal movement of the iron and the, side chain of the proximal tyrosine. Finally, the structure of the NADPH, complex shows that the cofactor is bound to the molecule in an equivalent, position to that found in beef liver catalase, but that only the adenine, part of NADPH is visible in the present structure.
+The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.
 ==About this Structure==
-GWF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Micrococcus_luteus Micrococcus luteus] with SO4, ACT, HEM and O as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GWF OCA].
+GWF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Micrococcus_luteus Micrococcus luteus] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=ACT:'>ACT</scene>, <scene name='pdbligand=HEM:'>HEM</scene> and <scene name='pdbligand=O:'>O</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GWF OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Micrococcus luteus]]
 [[Category: Single protein]]
-[[Category: Antson, A.A.]]
+[[Category: Antson, A A.]]
-[[Category: Barynin, V.V.]]
+[[Category: Barynin, V V.]]
-[[Category: Brannigan, J.A.]]
+[[Category: Brannigan, J A.]]
 [[Category: Dauter, Z.]]
-[[Category: Dodson, G.G.]]
+[[Category: Dodson, G G.]]
-[[Category: Grebenko, A.I.]]
+[[Category: Grebenko, A I.]]
-[[Category: Melik-Adamyan, W.R.]]
+[[Category: Melik-Adamyan, W R.]]
-[[Category: Murshudov, G.N.]]
+[[Category: Murshudov, G N.]]
-[[Category: Wilson, K.S.]]
+[[Category: Wilson, K S.]]
 [[Category: ACT]]
 [[Category: HEM]]
@@ Line 30: / Line 30: @@
 [[Category: hydrogen peroxide oxidoreductase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 16:19:22 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:54:42 2008''