8S5F

Crystal structure of the HExxH domain of ChlBHExxH a novel alpha-ketoglutarate dependent oxygenase

Summary for 8S5F

• Entry DOI: 10.2210/pdb8s5f/pdb
• Descriptor: ChlH from Chlorogloeopsis sp., PHOSPHATE ION (2 entities in total)
• Functional Keywords: alpha ketoglutarate dependent oxygenase hexxh domain ripps cyclophane, oxidoreductase
• Biological source: Chlorogloeopsis sp.
• Total number of polymer chains: 6
• Total formula weight: 251140.30

Authors

de la Mora, E.,Amara, P.,Usclat, A.,Morishita, Y.,Morinaka, B.,Nicolet, Y. (deposition date: 2024-02-23, release date: 2024-10-02, Last modification date: 2024-11-13)

Primary citation

Morishita, Y.,Ma, S.,De La Mora, E.,Li, H.,Chen, H.,Ji, X.,Usclat, A.,Amara, P.,Sugiyama, R.,Tooh, Y.W.,Gunawan, G.,Perard, J.,Nicolet, Y.,Zhang, Q.,Morinaka, B.I.
Fused radical SAM and alpha KG-HExxH domain proteins contain a distinct structural fold and catalyse cyclophane formation and beta-hydroxylation.
Nat.Chem., 16:1882-1893, 2024

PubMed Abstract: Two of nature's recurring binding motifs in metalloproteins are the CxxxCxxC motif in radical SAM enzymes and the 2-His-1-carboxylate motif found both in zincins and α-ketoglutarate and non-haem iron enzymes. Here we show the confluence of these two domains in a single post-translational modifying enzyme containing an N-terminal radical S-adenosylmethionine domain fused to a C-terminal 2-His-1-carboxylate (HExxH) domain. The radical SAM domain catalyses three-residue cyclophane formation and is the signature modification of triceptides, a class of ribosomally synthesized and post-translationally modified peptides. The HExxH domain is a defining feature of zinc metalloproteases. Yet the HExxH motif-containing domain studied here catalyses β-hydroxylation and is an α-ketoglutarate non-haem iron enzyme. We determined the crystal structure for this HExxH protein at 2.8 Å, unveiling a distinct structural fold, thus expanding the family of α-ketoglutarate non-haem iron enzymes with a class that we propose to name αKG-HExxH. αKG-HExxH proteins represent a unique family of ribosomally synthesized and post-translationally modified peptide modifying enzymes that can furnish opportunities for genome mining, synthetic biology and enzymology.

PubMed: 39294420
DOI: 10.1038/s41557-024-01596-9

Experimental method

X-RAY DIFFRACTION (2.797 Å)