6DNT

UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with UDP-N-acetylmuramic acid

Summary for 6DNT

• Entry DOI: 10.2210/pdb6dnt/pdb
• Descriptor: NAD-dependent epimerase/dehydratase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid, ... (6 entities in total)
• Functional Keywords: udp-n-acetylglucosamine, wbpp, 4-epimerase, udp-n-acetylmuramic acid, sugar binding protein
• Biological source: Methanobrevibacter ruminantium (strain ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1) (Methanobacterium ruminantium)
• Total number of polymer chains: 1
• Total formula weight: 40292.08

Authors

Carbone, V.,Schofield, L.R.,Sang, C.,Sutherland-Smith, A.J.,Ronimus, R.S. (deposition date: 2018-06-07, release date: 2018-10-03, Last modification date: 2023-10-11)

Primary citation

Carbone, V.,Schofield, L.R.,Sang, C.,Sutherland-Smith, A.J.,Ronimus, R.S.
Structural determination of archaeal UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with the bacterial cell wall intermediate UDP-N-acetylmuramic acid.
Proteins, 86:1306-1312, 2018

PubMed Abstract: The crystal structure of UDP-N-acetylglucosamine 4-epimerase (UDP-GlcNAc 4-epimerase; WbpP; EC 5.1.3.7), from the archaeal methanogen Methanobrevibacter ruminantium strain M1, was determined to a resolution of 1.65 Å. The structure, with a single monomer in the crystallographic asymmetric unit, contained a conserved N-terminal Rossmann-fold for nucleotide binding and an active site positioned in the C-terminus. UDP-GlcNAc 4-epimerase is a member of the short-chain dehydrogenases/reductases superfamily, sharing sequence motifs and structural elements characteristic of this family of oxidoreductases and bacterial 4-epimerases. The protein was co-crystallized with coenzyme NADH and UDP-N-acetylmuramic acid, the latter an unintended inclusion and well known product of the bacterial enzyme MurB and a critical intermediate for bacterial cell wall synthesis. This is a non-native UDP sugar amongst archaea and was most likely incorporated from the E. coli expression host during purification of the recombinant enzyme.

PubMed: 30242905
DOI: 10.1002/prot.25606

Experimental method

X-RAY DIFFRACTION (1.66 Å)