4X7G

CobK precorrin-6A reductase

Summary for 4X7G

• Entry DOI: 10.2210/pdb4x7g/pdb
• Related: 5C4R
• Descriptor: Precorrin-6A reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 3-[(1R,2S,3S,7S,11S,16S,17R,18R,19R)-2,7,12,18-tetrakis(2-hydroxy-2-oxoethyl)-3,13-bis(3-hydroxy-3-oxopropyl)-1,2,5,7,11,17-hexamethyl-17-(3-oxidanyl-3-oxidanylidene-prop-1-enyl)-3,6,8,10,15,16,18,19,21,24-decahydrocorrin-8-yl]propanoic acid, ... (4 entities in total)
• Functional Keywords: oxidoreductase, nadp binding
• Biological source: Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
• Total number of polymer chains: 1
• Total formula weight: 27873.94

Authors

Gu, S.,Deery, E.,Warren, M.J.,Pickersgill, R.W. (deposition date: 2014-12-09, release date: 2016-01-20, Last modification date: 2024-10-23)

Primary citation

Gu, S.,Sushko, O.,Deery, E.,Warren, M.J.,Pickersgill, R.W.
Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap.
Sci Rep, 5:16943-, 2015

PubMed Abstract: CobK catalyzes the essential reduction of the precorrin ring in the cobalamin biosynthetic pathway. The crystal structure of CobK reveals that the enzyme, despite not having the signature sequence, comprises two Rossmann fold domains which bind coenzyme and substrate respectively. The two parallel β-sheets have swapped their last β-strands giving a novel sheet topology which is an interesting variation on the Rossmann-fold. The trapped ternary complex with coenzyme and product reveals five conserved basic residues that bind the carboxylates of the tetrapyrrole tightly anchoring the product. A loop, disordered in both the apoenzyme and holoenzyme structures, closes around the product further tightening binding. The structure is consistent with a mechanism involving protonation of C18 and pro-R hydride transfer from NADPH to C19 of precorrin-6A and reveals the interactions responsible for the specificity of CobK. The almost complete burial of the reduced precorrin product suggests a remarkable form of metabolite channeling where the next enzyme in the biosynthetic pathway triggers product release.

PubMed: 26616290
DOI: 10.1038/srep16943

Experimental method

X-RAY DIFFRACTION (1.22 Å)