1r76: Difference between revisions

Revision as of 07:10, 3 May 2008

Structure of a pectate lyase from Azospirillum irakense

OverviewOverview

The three-dimensional structure of Azospirillum irakense pectate lyase (PelA) has been determined at a resolution of 2.65 A. The crystals are hexagonal, belonging to space group P6(5)22, with unit-cell parameters a = b = 85.37, c = 231.32 angstroms. Phase information was derived from a multiple-wavelength anomalous dispersion (MAD) experiment using a Hg derivative. Refinement of the model converged to Rcryst = 20.08% and Rfree = 25.87%. The overall structure of PelA does not adopt the characteristic parallel beta-helix fold displayed by pectate lyases from polysaccharide lyase (PL) families PL1, PL3 and PL9. Instead, it displays a predominantly alpha-helical structure with irregular coils and short beta-strands, similar to the recently reported structure of the catalytic module of the Cellvibrio japonicus pectate lyase Pel10Acm. The topologies of the two structures have been compared. They show two 'domains' with the interface between them being a wide-open central groove in which the active site is located. The active sites of the crystal structures are also compared and their similarities and differences are discussed.

About this StructureAbout this Structure

1R76 is a Single protein structure of sequence from Azospirillum irakense. Full crystallographic information is available from OCA.

ReferenceReference

Azospirillum irakense pectate lyase displays a toroidal fold., Novoa De Armas H, Verboven C, De Ranter C, Desair J, Vande Broek A, Vanderleyden J, Rabijns A, Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):999-1007. Epub 2004, May 21. PMID:15159558 Page seeded by OCA on Sat May 3 07:10:02 2008

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OCA

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 [[Image:1r76.jpg|left|200px]]
- {{Structure
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+The line below this paragraph, containing "STRUCTURE_1r76", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= pelA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34011 Azospirillum irakense])
+-->
-|DOMAIN=
+{{STRUCTURE_1r76|  PDB=1r76  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r76 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r76 OCA], [http://www.ebi.ac.uk/pdbsum/1r76 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r76 RCSB]</span>
-}}
 '''Structure of a pectate lyase from Azospirillum irakense'''
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 [[Category: Vanderleyden, J.]]
 [[Category: Verboven, C.]]
-[[Category: a-helical structure]]
+[[Category: A-helical structure]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 07:10:02 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:24:11 2008''