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1lga

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(New page: 200px<br /><applet load="1lga" size="450" color="white" frame="true" align="right" spinBox="true" caption="1lga, resolution 2.03&Aring;" /> '''CRYSTALLOGRAPHIC REF...)
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[[Image:1lga.gif|left|200px]]<br /><applet load="1lga" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1lga, resolution 2.03&Aring;" />
 
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'''CRYSTALLOGRAPHIC REFINEMENT OF LIGNIN PEROXIDASE AT 2 ANGSTROMS'''<br />
 
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==Overview==
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==CRYSTALLOGRAPHIC REFINEMENT OF LIGNIN PEROXIDASE AT 2 ANGSTROMS==
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The crystal structure of the major lignin peroxidase isozyme from, Phanerocheate chrysosporium has been refined to an R = 0.15 for data, between 8 A and 2.03 A. The refined model consists of 2 lignin peroxidase, molecules in the asymmetric unit, 2 calcium ions per monomer, 1, glucosamine per monomer N-linked to Asn-257, and 476 water molecules per, asymmetric unit. The model exhibits excellent geometry with a root mean, square deviation from ideality in bond distances and angles of 0.014 A and, 2.9 degrees, respectively. Molecule 1 consists of all 343 residues, while, molecule 2 consists of residues 1-341. The overall root mean square, deviation in backbone atoms between the 2 molecules in the asymmetric unit, is 0.36 A. The refinement at 2.0 A confirms our conclusions based on the, partially refined 2.6-A structure (Edwards, S. L., Raag, R., Wariishi, H., Gold, M. H., and Poulos, T. L. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 750-754). The overall fold of lignin peroxidase closely resembles that of, cytochrome c peroxidase. A superimposition of alpha-carbons gives a root, mean square deviation of 2.65 A between the two peroxidases and 1.66 A for, the helices. The active sites also are similar since both contain a, proximal histidine heme ligand hydrogen-bonded to a buried aspartate, residue and both contain histidine and arginine residues in the distal, peroxide binding pocket. The most obvious difference in the active site is, that whereas cytochrome c peroxidase has tryptophan residues located in, the proximal and distal heme pockets, lignin peroxidase has, phenylalanines. There are four other especially noteworthy differences in, the two structures. First, although the heme in cytochrome c peroxidase is, recessed about 10 A from the molecular surface, the heme pocket is open to, solvent. The analogous opening in lignin peroxidase is smaller which can, explain in part the differences in reactivity of the two hemes. This same, opening may provide the site for binding small aromatic substrates., Second, lignin peroxidase has a carboxylate-carboxylate hydrogen bond, important for heme binding that is not present in cytochrome c peroxidase., Third, lignin peroxidase contains 2 structural calcium ions while, cytochrome c peroxidase contains no calcium. The calciums in lignin, peroxidase coordinate to residues near the C-terminal ends of the distal, and proximal helices and hence are probably important for maintaining the, integrity of the active site. Fourth, the extra 49 residues in lignin, peroxidase not present in cytochrome c peroxidase constitutes the, C-terminal end of the molecule with the C terminus situated at the "front", end of the molecule between the two heme propionates.
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<StructureSection load='1lga' size='340' side='right'caption='[[1lga]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1lga]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phanerodontia_chrysosporium Phanerodontia chrysosporium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LGA FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lga OCA], [https://pdbe.org/1lga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lga RCSB], [https://www.ebi.ac.uk/pdbsum/1lga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lga ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LIG2_PHACH LIG2_PHACH] Depolymerization of lignin. Catalyzes the C(alpha)-C(beta) cleavage of the propyl side chains of lignin.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lg/1lga_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lga ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1LGA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Phanerochaete_chrysosporium Phanerochaete chrysosporium] with NAG, CA and HEM as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LGA OCA].
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*[[Lignin peroxidase|Lignin peroxidase]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystallographic refinement of lignin peroxidase at 2 A., Poulos TL, Edwards SL, Wariishi H, Gold MH, J Biol Chem. 1993 Feb 25;268(6):4429-40. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8440725 8440725]
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[[Category: Large Structures]]
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[[Category: Phanerochaete chrysosporium]]
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[[Category: Phanerodontia chrysosporium]]
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[[Category: Single protein]]
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[[Category: Edwards SL]]
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[[Category: Edwards, S.L.]]
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[[Category: Gold MH]]
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[[Category: Gold, M.H.]]
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[[Category: Poulos TL]]
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[[Category: Poulos, T.L.]]
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[[Category: Wariishi H]]
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[[Category: Wariishi, H.]]
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[[Category: CA]]
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[[Category: HEM]]
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[[Category: NAG]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:32:39 2007''
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Current revision

CRYSTALLOGRAPHIC REFINEMENT OF LIGNIN PEROXIDASE AT 2 ANGSTROMS

PDB ID 1lga

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