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6Z6R

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, N-oxalyl-alpha-methylalanine, and factor X substrate peptide fragment(39mer-4Ser)

Summary for 6Z6R
Entry DOI10.2210/pdb6z6r/pdb
DescriptorAspartyl/asparaginyl beta-hydroxylase, Coagulation factor X, MANGANESE (II) ION, ... (7 entities in total)
Functional Keywordsaspartyl/asparaginyl beta-hydroxylase, dioxygenase, oxidoreductase
Biological sourceHomo sapiens (Human)
More
Total number of polymer chains2
Total formula weight53997.80
Authors
Nakashima, Y.,Brewitz, L.,Schofield, C.J. (deposition date: 2020-05-29, release date: 2021-03-17, Last modification date: 2024-10-16)
Primary citationBrewitz, L.,Nakashima, Y.,Schofield, C.J.
Synthesis of 2-oxoglutarate derivatives and their evaluation as cosubstrates and inhibitors of human aspartate/asparagine-beta-hydroxylase.
Chem Sci, 12:1327-1342, 2020
Cited by
PubMed Abstract: 2-Oxoglutarate (2OG) is involved in biological processes including oxidations catalyzed by 2OG oxygenases for which it is a cosubstrate. Eukaryotic 2OG oxygenases have roles in collagen biosynthesis, lipid metabolism, DNA/RNA modification, transcriptional regulation, and the hypoxic response. Aspartate/asparagine-β-hydroxylase (AspH) is a human 2OG oxygenase catalyzing post-translational hydroxylation of Asp/Asn-residues in epidermal growth factor-like domains (EGFDs) in the endoplasmic reticulum. AspH is of chemical interest, because its Fe(ii) cofactor is complexed by two rather than the typical three residues. AspH is upregulated in hypoxia and is a prognostic marker on the surface of cancer cells. We describe studies on how derivatives of its natural 2OG cosubstrate modulate AspH activity. An efficient synthesis of C3- and/or C4-substituted 2OG derivatives, proceeding cyanosulfur ylid intermediates, is reported. Mass spectrometry-based AspH assays with >30 2OG derivatives reveal that some efficiently inhibit AspH competing with 2OG as evidenced by crystallographic and solution analyses. Other 2OG derivatives can substitute for 2OG enabling substrate hydroxylation. The results show that subtle changes, methyl- to ethyl-substitution, can significantly alter the balance between catalysis and inhibition. 3-Methyl-2OG, a natural product present in human nutrition, was the most efficient alternative cosubstrate identified; crystallographic analyses reveal the binding mode of ()-3-methyl-2OG and other 2OG derivatives to AspH and inform on the balance between turnover and inhibition. The results will enable the use of 2OG derivatives as mechanistic probes for other 2OG utilizing enzymes and suggest 2-oxoacids other than 2OG may be employed by some 2OG oxygenases .
PubMed: 34163896
DOI: 10.1039/d0sc04301j
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.13 Å)
Structure validation

226707

数据于2024-10-30公开中

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