2i56
From Proteopedia
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|PDB= 2i56 |SIZE=350|CAPTION= <scene name='initialview01'>2i56</scene>, resolution 1.97Å | |PDB= 2i56 |SIZE=350|CAPTION= <scene name='initialview01'>2i56</scene>, resolution 1.97Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=RNS:L-RHAMNOSE'>RNS</scene> | + | |LIGAND= <scene name='pdbligand=RNS:L-RHAMNOSE'>RNS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/L-rhamnose_isomerase L-rhamnose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.14 5.3.1.14] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/L-rhamnose_isomerase L-rhamnose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.14 5.3.1.14] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2hcv|2HCV]], [[2i57|2I57]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2i56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i56 OCA], [http://www.ebi.ac.uk/pdbsum/2i56 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2i56 RCSB]</span> | ||
}} | }} | ||
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[[Category: Yamada, M.]] | [[Category: Yamada, M.]] | ||
[[Category: Yoshida, H.]] | [[Category: Yoshida, H.]] | ||
| - | [[Category: RNS]] | ||
| - | [[Category: ZN]] | ||
[[Category: beta/alpha barrel]] | [[Category: beta/alpha barrel]] | ||
[[Category: homo-tetramer]] | [[Category: homo-tetramer]] | ||
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[[Category: tim barrel]] | [[Category: tim barrel]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:39:49 2008'' |
Revision as of 00:39, 31 March 2008
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| , resolution 1.97Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | L-rhamnose isomerase, with EC number 5.3.1.14 | ||||||
| Related: | 2HCV, 2I57
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose
Overview
Pseudomonas stutzeri L-rhamnose isomerase (P. stutzeri L-RhI) can efficiently catalyze the isomerization between various aldoses and ketoses, showing a broad substrate specificity compared to L-RhI from Escherichia coli (E. coli L-RhI). To understand the relationship between structure and substrate specificity, the crystal structures of P. stutzeri L-RhI alone and in complexes with L-rhamnose and D-allose which has different configurations of C4 and C5 from L-rhamnose, were determined at a resolution of 2.0 A, 1.97 A, and 1.97 A, respectively. P. stutzeri L-RhI has a large domain with a (beta/alpha)(8) barrel fold and an additional small domain composed of seven alpha-helices, forming a homo tetramer, as found in E. coli L-RhI and D-xylose isomerases (D-XIs) from various microorganisms. The beta1-alpha1 loop (Gly60-Arg76) of P. stutzeri L-RhI is involved in the substrate binding of a neighbouring molecule, as found in D-XIs, while in E. coli L-RhI, the corresponding beta1-alpha1 loop is extended (Asp52-Arg78) and covers the substrate-binding site of the same molecule. The complex structures of P. stutzeri L-RhI with L-rhamnose and D-allose show that both substrates are nicely fitted to the substrate-binding site. The part of the substrate-binding site interacting with the substrate at the 1, 2, and 3 positions is equivalent to E. coli L-RhI, and the other part interacting with the 4, 5, and 6 positions is similar to D-XI. In E. coli L-RhI, the beta1-alpha1 loop creates an unique hydrophobic pocket at the the 4, 5, and 6 positions, leading to the strictly recognition of L-rhamnose as the most suitable substrate, while in P. stutzeri L-RhI, there is no corresponding hydrophobic pocket where Phe66 from a neighbouring molecule merely forms hydrophobic interactions with the substrate, leading to the loose substrate recognition at the 4, 5, and 6 positions.
About this Structure
2I56 is a Single protein structure of sequence from Pseudomonas stutzeri. Full crystallographic information is available from OCA.
Reference
The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity., Yoshida H, Yamada M, Ohyama Y, Takada G, Izumori K, Kamitori S, J Mol Biol. 2007 Feb 2;365(5):1505-16. Epub 2006 Nov 6. PMID:17141803
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