1a05
From Proteopedia
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|PDB= 1a05 |SIZE=350|CAPTION= <scene name='initialview01'>1a05</scene>, resolution 2.00Å | |PDB= 1a05 |SIZE=350|CAPTION= <scene name='initialview01'>1a05</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=IPM:3-ISOPROPYLMALIC+ACID'>IPM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/3-isopropylmalate_dehydrogenase 3-isopropylmalate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.85 1.1.1.85] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/3-isopropylmalate_dehydrogenase 3-isopropylmalate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.85 1.1.1.85] </span> |
|GENE= LEUB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=920 Acidithiobacillus ferrooxidans]) | |GENE= LEUB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=920 Acidithiobacillus ferrooxidans]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1a05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a05 OCA], [http://www.ebi.ac.uk/pdbsum/1a05 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1a05 RCSB]</span> | ||
}} | }} | ||
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[[Category: Tanaka, H.]] | [[Category: Tanaka, H.]] | ||
[[Category: Tanaka, N.]] | [[Category: Tanaka, N.]] | ||
| - | [[Category: IPM]] | ||
| - | [[Category: MG]] | ||
[[Category: decarboxylating dehydrogenase]] | [[Category: decarboxylating dehydrogenase]] | ||
[[Category: leucine biosynthesis]] | [[Category: leucine biosynthesis]] | ||
[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:30:17 2008'' |
Revision as of 15:30, 30 March 2008
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| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | LEUB (Acidithiobacillus ferrooxidans) | ||||||
| Activity: | 3-isopropylmalate dehydrogenase, with EC number 1.1.1.85 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE
Overview
BACKGROUND: 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding. RESULTS: We have determined the crystal structure of IPMDH from Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at 2.0 A resolution by the molecular replacement method. The structure shows a fully closed conformation and the substrate-binding site is quite similar to that of ICDH except for a region around the gamma-isopropyl group. The gamma group is recognized by a unique hydrophobic pocket, which includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2. CONCLUSIONS: A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the gamma-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The C beta and C gamma atoms of Glu88 interact with the gamma-isopropyl moiety of IPM and are central to the recognition of substrate. The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH.
About this Structure
1A05 is a Single protein structure of sequence from Acidithiobacillus ferrooxidans. Full crystallographic information is available from OCA.
Reference
Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism., Imada K, Inagaki K, Matsunami H, Kawaguchi H, Tanaka H, Tanaka N, Namba K, Structure. 1998 Aug 15;6(8):971-82. PMID:9739088
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