1ylh: Difference between revisions

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Crystal Structure of Phosphoenolpyruvate Carboxykinase from Actinobaccilus succinogenes in Complex with Manganese and Pyruvate

OverviewOverview

Actinobacillus succinogenes can produce, via fermentation, high concentrations of succinate, an important industrial commodity. A key enzyme in this pathway is phosphoenolpyruvate carboxykinase (PCK), which catalyzes the production of oxaloacetate from phosphoenolpyruvate and carbon dioxide, with the concomitant conversion of adenosine 5'-diphosphate to adenosine 5'-triphosphate. 1.85 and 1.70 A resolution structures of the native and a pyruvate/Mn(2+)/phosphate complex have been solved, respectively. The structure of the complex contains sulfhydryl reducing agents covalently bound to three cysteine residues via disulfide bonds. One of these cysteine residues (Cys285) is located in the active-site cleft and may be analogous to the putative reactive cysteine of PCK from Trypanosoma cruzi. Cys285 is also part of a previously unreported conserved motif comprising residues 280-287 and containing the pattern NXEXGXY(/F)A(/G); this new motif appears to have a structural role in stabilizing and positioning side chains that bind substrates and metal ions. The first few residues of this motif connect the two domains of the enzyme and a fulcrum point appears to be located near Asn280. In addition, an active-site Asp residue forms two coordinate bonds with the Mn(2+) ion present in the structure of the complex in a symmetrical bidentate manner, unlike in other PCK structures that contain a manganese ion.

About this StructureAbout this Structure

1YLH is a Single protein structure of sequence from Actinobacillus succinogenes. Full crystallographic information is available from OCA.

ReferenceReference

Structure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif., Leduc YA, Prasad L, Laivenieks M, Zeikus JG, Delbaere LT, Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):903-12. Epub 2005, Jun 24. PMID:15983413 Page seeded by OCA on Sat May 3 16:28:25 2008

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OCA

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 [[Image:1ylh.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1ylh |SIZE=350|CAPTION= <scene name='initialview01'>1ylh</scene>, resolution 1.70&Aring;
+The line below this paragraph, containing "STRUCTURE_1ylh", 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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=DT3:(2S,3S)-2,3-DIHYDROXY-4-SULFANYLBUTANE-1-SULFONATE'>DT3</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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/Phosphoenolpyruvate_carboxykinase_(ATP) Phosphoenolpyruvate carboxykinase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.49 4.1.1.49] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= PCKA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=67854 Actinobacillus succinogenes])
+-->
-|DOMAIN=
+{{STRUCTURE_1ylh|  PDB=1ylh  |  SCENE=  }}
-|RELATEDENTRY=[[1ygg|1YGG]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ylh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ylh OCA], [http://www.ebi.ac.uk/pdbsum/1ylh PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ylh RCSB]</span>
-}}
 '''Crystal Structure of Phosphoenolpyruvate Carboxykinase from Actinobaccilus succinogenes in Complex with Manganese and Pyruvate'''
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 Structure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif., Leduc YA, Prasad L, Laivenieks M, Zeikus JG, Delbaere LT, Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):903-12. Epub 2005, Jun 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15983413 15983413]
 [[Category: Actinobacillus succinogenes]]
-[[Category: Phosphoenolpyruvate carboxykinase (ATP)]]
 [[Category: Single protein]]
 [[Category: Delbaere, L T.]]
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 [[Category: Prasad, L.]]
 [[Category: Zeikus, J G.]]
-[[Category: bound sulfhydrl reducing agent]]
+[[Category: Bound sulfhydrl reducing agent]]
-[[Category: disulphide bond]]
+[[Category: Disulphide bond]]
-[[Category: phosphoenolpyruvate carboxykinase]]
+[[Category: Phosphoenolpyruvate carboxykinase]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 16:28:25 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:12:02 2008''