1hye
From Proteopedia
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|PDB= 1hye |SIZE=350|CAPTION= <scene name='initialview01'>1hye</scene>, resolution 1.90Å | |PDB= 1hye |SIZE=350|CAPTION= <scene name='initialview01'>1hye</scene>, resolution 1.90Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NAP:NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE'>NAP</scene> | + | |LIGAND= <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span> |
|GENE= MJ0490 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii]) | |GENE= MJ0490 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1hyg|1HYG]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1hye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hye OCA], [http://www.ebi.ac.uk/pdbsum/1hye PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1hye RCSB]</span> | ||
}} | }} | ||
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[[Category: Lee, B I.]] | [[Category: Lee, B I.]] | ||
[[Category: Suh, S W.]] | [[Category: Suh, S W.]] | ||
| - | [[Category: NAP]] | ||
[[Category: nucleotide binding domain]] | [[Category: nucleotide binding domain]] | ||
| - | ''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 21:11:57 2008'' |
Revision as of 18:11, 30 March 2008
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| , resolution 1.90Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | MJ0490 (Methanocaldococcus jannaschii) | ||||||
| Activity: | L-lactate dehydrogenase, with EC number 1.1.1.27 | ||||||
| Related: | 1HYG
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE MJ0490 GENE PRODUCT, THE FAMILY OF LACTATE/MALATE DEHYDROGENASE, DIMERIC STRUCTURE
Overview
The MJ0490 gene, one of the only two genes of Methanococcus jannaschii showing sequence similarity to the lactate/malate family of dehydrogenases, was classified initially as coding for a putative l-lactate dehydrogenase (LDH). It has been re-classified as a malate dehydrogenase (MDH) gene, because it shows significant sequence similarity to MT0188, MDH II from Methanobacterium thermoautotrophicum strain DeltaH. The three-dimensional structure of its gene product has been determined in two crystal forms: a "dimeric" structure in the orthorhombic crystal at 1.9 A resolution and a "tetrameric" structure in the tetragonal crystal at 2.8 A. These structures share a similar subunit fold with other LDHs and MDHs. The tetrameric structure resembles typical tetrameric LDHs. The dimeric structure is equivalent to the P-dimer of tetrameric LDHs, unlike dimeric MDHs, which correspond to the Q-dimer. The structure reveals that the cofactor NADP(H) is bound at the active site, despite the fact that it was not intentionally added during protein purification and crystallization. The preference of NADP(H) over NAD(H) has been supported by activity assays. The cofactor preference is explained by the presence of a glycine residue in the cofactor binding pocket (Gly33), which replaces a conserved aspartate (or glutamate) residue in other NAD-dependent LDHs or MDHs. Preference for NADP(H) is contributed by hydrogen bonds between the oxygen atoms of the monophosphate group and the ribose sugar of adenosine in NADP(H) and the side-chains of Ser9, Arg34, His36, and Ser37. The MDH activity of MJ0490 is made possible by Arg86, which is conserved in MDHs but not in LDHs. The enzymatic assay showed that the MJ0490 protein possesses the fructose-1,6-bisphosphate-activated LDH activity (reduction). Thus the MJ0490 gene product appears to be a novel member of the lactate/malate dehydrogenase family, displaying an LDH scaffold and exhibiting a relaxed substrate and cofactor specificities in NADP(H) and NAD(H)-dependent malate and lactate dehydrogenase reactions.
About this Structure
1HYE is a Single protein structure of sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA.
Reference
Crystal structure of the MJ0490 gene product of the hyperthermophilic archaebacterium Methanococcus jannaschii, a novel member of the lactate/malate family of dehydrogenases., Lee BI, Chang C, Cho SJ, Eom SH, Kim KK, Yu YG, Suh SW, J Mol Biol. 2001 Apr 13;307(5):1351-62. PMID:11292347
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