2mnr
From Proteopedia
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| - | [[Image:2mnr.gif|left|200px]] | + | [[Image:2mnr.gif|left|200px]] |
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| - | '''MECHANISM OF THE REACTION CATALYZED BY MANDELATE RACEMASE. 2. CRYSTAL STRUCTURE OF MANDELATE RACEMASE AT 2.5 ANGSTROMS RESOLUTION: IDENTIFICATION OF THE ACTIVE SITE AND POSSIBLE CATALYTIC RESIDUES''' | + | {{Structure |
| + | |PDB= 2mnr |SIZE=350|CAPTION= <scene name='initialview01'>2mnr</scene>, resolution 1.9Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> and <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Mandelate_racemase Mandelate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.2.2 5.1.2.2] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''MECHANISM OF THE REACTION CATALYZED BY MANDELATE RACEMASE. 2. CRYSTAL STRUCTURE OF MANDELATE RACEMASE AT 2.5 ANGSTROMS RESOLUTION: IDENTIFICATION OF THE ACTIVE SITE AND POSSIBLE CATALYTIC RESIDUES''' | ||
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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2MNR is a [ | + | 2MNR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MNR OCA]. |
==Reference== | ==Reference== | ||
| - | Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues., Neidhart DJ, Howell PL, Petsko GA, Powers VM, Li RS, Kenyon GL, Gerlt JA, Biochemistry. 1991 Sep 24;30(38):9264-73. PMID:[http:// | + | Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues., Neidhart DJ, Howell PL, Petsko GA, Powers VM, Li RS, Kenyon GL, Gerlt JA, Biochemistry. 1991 Sep 24;30(38):9264-73. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1892834 1892834] |
[[Category: Mandelate racemase]] | [[Category: Mandelate racemase]] | ||
[[Category: Pseudomonas putida]] | [[Category: Pseudomonas putida]] | ||
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[[Category: racemase]] | [[Category: racemase]] | ||
| - | ''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 17:47:28 2008'' |
Revision as of 15:47, 20 March 2008
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| , resolution 1.9Å | |||||||
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| Ligands: | and | ||||||
| Activity: | Mandelate racemase, with EC number 5.1.2.2 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
MECHANISM OF THE REACTION CATALYZED BY MANDELATE RACEMASE. 2. CRYSTAL STRUCTURE OF MANDELATE RACEMASE AT 2.5 ANGSTROMS RESOLUTION: IDENTIFICATION OF THE ACTIVE SITE AND POSSIBLE CATALYTIC RESIDUES
Overview
The crystal structure of mandelate racemase (MR) has been solved at 3.0-A resolution by multiple isomorphous replacement and subsequently refined against X-ray diffraction data to 2.5-A resolution by use of both molecular dynamics refinement (XPLOR) and restrained least-squares refinement (PROLSQ). The current crystallographic R-factor for this structure is 18.3%. MR is composed of two major structural domains and a third, smaller, C-terminal domain. The N-terminal domain has an alpha + beta topology consisting of a three-stranded antiparallel beta-sheet followed by an antiparallel four alpha-helix bundle. The central domain is a singly wound parallel alpha/beta-barrel composed of eight central strands of beta-sheet and seven alpha-helices. The C-terminal domain consists of an irregular L-shaped loop with several short sections of antiparallel beta-sheet and two short alpha-helices. This C-terminal domain partially covers the junction between the major domains and occupies a region of the central domain that is filled by an eight alpha-helix in all other known parallel alpha/beta-barrels except for the barrel domain in muconate lactonizing enzyme (MLE) [Goldman, A., Ollis, D. L., & Steitz, T. A. (1987) J. Mol. Biol. 194, 143] whose overall polypeptide fold and amino acid sequence are strikingly similar to those of MR [Neidhart, D. J., Kenyon, G. L., Gerlt, J. A., & Petsko, G. A. (1990) Nature 347, 692]. In addition, the crystal structure reveals that, like MLE, MR is tightly packed as an octamer of identical subunits. The active site of MR is located between the two major domains, at the C-terminal ends of the beta-strands in the alpha/beta-barrel domain. The catalytically essential divalent metal ion is ligated by three side-chain carboxyl groups contributed by residues of the central beta-sheet. A model of a productive substrate complex of MR has been constructed on the basis of difference Fourier analysis at 3.5-A resolution of a complex between MR and (R,S)-p-iodomandelate, permitting identification of residues that may participate in substrate binding and catalysis. The ionizable groups of both Lys 166 and His 297 are positioned to interact with the chiral center of substrate, suggesting that both of these residues may function as acid/base catalysts.(ABSTRACT TRUNCATED AT 400 WORDS)
About this Structure
2MNR is a Single protein structure of sequence from Pseudomonas putida. Full crystallographic information is available from OCA.
Reference
Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues., Neidhart DJ, Howell PL, Petsko GA, Powers VM, Li RS, Kenyon GL, Gerlt JA, Biochemistry. 1991 Sep 24;30(38):9264-73. PMID:1892834
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