3b8i
From Proteopedia
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| - | [[Image:3b8i.jpg|left|200px]] | + | [[Image:3b8i.jpg|left|200px]] |
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| - | '''Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.''' | + | {{Structure |
| + | |PDB= 3b8i |SIZE=350|CAPTION= <scene name='initialview01'>3b8i</scene>, resolution 1.90Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Oxaloacetate_decarboxylase Oxaloacetate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.3 4.1.1.3] | ||
| + | |GENE= Dnase1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.''' | ||
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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 3B8I is a [ | + | 3B8I is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8I OCA]. |
==Reference== | ==Reference== | ||
| - | Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily., Narayanan BC, Niu W, Han Y, Zou J, Mariano PS, Dunaway-Mariano D, Herzberg O, Biochemistry. 2008 Jan 8;47(1):167-82. Epub 2007 Dec 15. PMID:[http:// | + | Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily., Narayanan BC, Niu W, Han Y, Zou J, Mariano PS, Dunaway-Mariano D, Herzberg O, Biochemistry. 2008 Jan 8;47(1):167-82. Epub 2007 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18081320 18081320] |
[[Category: Oxaloacetate decarboxylase]] | [[Category: Oxaloacetate decarboxylase]] | ||
[[Category: Pseudomonas aeruginosa]] | [[Category: Pseudomonas aeruginosa]] | ||
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[[Category: lyase]] | [[Category: lyase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:57:05 2008'' |
Revision as of 16:57, 20 March 2008
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| , resolution 1.90Å | |||||||
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| Ligands: | , and | ||||||
| Gene: | Dnase1 (Pseudomonas aeruginosa) | ||||||
| Activity: | Oxaloacetate decarboxylase, with EC number 4.1.1.3 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.
Overview
Pseudomonas aeruginosa PA4872 was identified by sequence analysis as a structurally and functionally novel member of the PEP mutase/isocitrate lyase superfamily and therefore targeted for investigation. Substrate screens ruled out overlap with known catalytic functions of superfamily members. The crystal structure of PA4872 in complex with oxalate (a stable analogue of the shared family alpha-oxyanion carboxylate intermediate/transition state) and Mg2+ was determined at 1.9 A resolution. As with other PEP mutase/isocitrate lyase superfamily members, the protein assembles into a dimer of dimers with each subunit adopting an alpha/beta barrel fold and two subunits swapping their barrel's C-terminal alpha-helices. Mg2+ and oxalate bind in the same manner as observed with other superfamily members. The active site gating loop, known to play a catalytic role in the PEP mutase and lyase branches of the superfamily, adopts an open conformation. The Nepsilon of His235, an invariant residue in the PA4872 sequence family, is oriented toward a C(2) oxygen of oxalate analogous to the C(3) of a pyruvyl moiety. Deuterium exchange into alpha-oxocarboxylate-containing compounds was confirmed by 1H NMR spectroscopy. Having ruled out known activities, the involvement of a pyruvate enolate intermediate suggested a decarboxylase activity of an alpha-oxocarboxylate substrate. Enzymatic assays led to the discovery that PA4872 decarboxylates oxaloacetate (kcat = 7500 s(-1) and Km = 2.2 mM) and 3-methyloxaloacetate (kcat = 250 s(-1) and Km = 0.63 mM). Genome context of the fourteen sequence family members indicates that the enzyme is used by select group of Gram-negative bacteria to maintain cellular concentrations of bicarbonate and pyruvate; however the decarboxylation activity cannot be attributed to a pathway common to the various bacterial species.
About this Structure
3B8I is a Single protein structure of sequence from Pseudomonas aeruginosa. Full crystallographic information is available from OCA.
Reference
Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily., Narayanan BC, Niu W, Han Y, Zou J, Mariano PS, Dunaway-Mariano D, Herzberg O, Biochemistry. 2008 Jan 8;47(1):167-82. Epub 2007 Dec 15. PMID:18081320
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