1x1t
From Proteopedia
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|PDB= 1x1t |SIZE=350|CAPTION= <scene name='initialview01'>1x1t</scene>, resolution 1.52Å | |PDB= 1x1t |SIZE=350|CAPTION= <scene name='initialview01'>1x1t</scene>, resolution 1.52Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1wmb|1WMB]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [http://www.ebi.ac.uk/pdbsum/1x1t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB]</span> | ||
}} | }} | ||
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[[Category: Ogawa, K.]] | [[Category: Ogawa, K.]] | ||
[[Category: Yoshimoto, T.]] | [[Category: Yoshimoto, T.]] | ||
| - | [[Category: CAC]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: NAD]] | ||
[[Category: beta-hydroxybutyrate]] | [[Category: beta-hydroxybutyrate]] | ||
[[Category: ketone body]] | [[Category: ketone body]] | ||
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[[Category: short chain dehydrogenase]] | [[Category: short chain dehydrogenase]] | ||
| - | ''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 00:43:45 2008'' |
Revision as of 21:43, 30 March 2008
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| , resolution 1.52Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | 3-hydroxybutyrate dehydrogenase, with EC number 1.1.1.30 | ||||||
| Related: | 1WMB
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+
Overview
The gene coding for d-3-hydroxybutyrate dehydrogenase (HBDH) was cloned from Pseudomonas fragi. The nucleotide sequence contained a 780 bp open reading frame encoding a 260 amino acid residue protein. The recombinant enzyme was efficiently expressed in Escherichia coli cells harboring pHBDH11 and was purified to homogeneity as judged by SDS-PAGE. The enzyme showed a strict stereospecificity to the D-enantiomer (3R-configuration) of 3-hydroxybutyrate as a substrate. Crystals of the ligand-free HBDH and of the enzyme-NAD+ complex were obtained using the hanging-drop, vapor-diffusion method. The crystal structure of the HBDH was solved by the multiwavelength anomalous diffraction method using the SeMet-substituted enzyme and was refined to 2.0 A resolution. The overall structure of P.fragi HBDH, including the catalytic tetrad of Asn114, Ser142, Tyr155, and Lys159, shows obvious relationships with other members of the short-chain dehydrogenase/reductase (SDR) family. A cacodylate anion was observed in both the ligand-free enzyme and the enzyme-NAD+ complex, and was located near the catalytic tetrad. It was shown that the cacodylate inhibited the NAD+-dependent D-3-hydroxybutyrate dehydrogenation competitively, with a Ki value of 5.6 mM. From the interactions between cacodylate and the enzyme, it is predicted that substrate specificity is achieved through the recognition of the 3-methyl and carboxyl groups of the substrate.
About this Structure
1X1T is a Single protein structure of sequence from Pseudomonas fragi. Full crystallographic information is available from OCA.
Reference
D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme., Ito K, Nakajima Y, Ichihara E, Ogawa K, Katayama N, Nakashima K, Yoshimoto T, J Mol Biol. 2006 Jan 27;355(4):722-33. Epub 2005 Nov 14. PMID:16325199
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