PDBsum entry 4zht

Isomerase

PDB id: 4zht

Contents

Protein chains

384 a.a.

Ligands

UDP ×4

NCC ×4

BM7

Waters ×331

PDB id:

4zht

Name:

Isomerase

Title:

Crystal structure of udp-glcnac 2-epimerase

Structure:

Bifunctional udp-n-acetylglucosamine 2-epimerase/n- acetylmannosamine kinase. Chain: a, b, c, d. Fragment: unp residues 1-405. Synonym: udp-glcnac-2-epimerase/manac kinase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: gne, glcne. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.69Å R-factor: 0.191 R-free: 0.225

Authors:

S.C.Chen,C.S.Yang,T.P.Ko,Y.Chen

Key ref:

S.C.Chen et al. (2016). Mechanism and inhibition of human UDP-GlcNAc 2-epimerase, the key enzyme in sialic acid biosynthesis. Sci Rep, 6, 23274. PubMed id: 26980148 DOI: 10.1038/srep23274

Date:

27-Apr-15 Release date: 01-Jun-16

Protein chains

Q9Y223  (GLCNE_HUMAN) -  Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase from Homo sapiens

Seq: 722 a.a.

Struc: 384 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.7.1.60 - N-acylmannosamine kinase.
• Reaction: an N-acyl-D-mannosamine + ATP = an N-acyl-D-mannosamine 6-phosphate + ADP + H⁺

N-acyl-D-mannosamine + ATP (Bound ligand (Het Group name = BM7) matches with 87.50% similarity) = N-acyl-D-mannosamine 6-phosphate (Bound ligand (Het Group name = UDP) matches with 79.31% similarity) + ADP + H(+)

• Enzyme class 3: E.C.3.2.1.183 - UDP-N-acetylglucosamine 2-epimerase (hydrolyzing).
• Reaction: UDP-N-acetyl-alpha-D-glucosamine + H2O = aldehydo-N-acetyl-D-mannosamine + UDP + H⁺

UDP-N-acetyl-alpha-D-glucosamine + H2O = aldehydo-N-acetyl-D-mannosamine (Bound ligand (Het Group name = BM7) corresponds exactly) + UDP (Bound ligand (Het Group name = UDP) corresponds exactly) + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/srep23274

Sci Rep 6:23274 (2016)

PubMed id: 26980148

Mechanism and inhibition of human UDP-GlcNAc 2-epimerase, the key enzyme in sialic acid biosynthesis.

S.C.Chen, C.H.Huang, S.J.Lai, C.S.Yang, T.H.Hsiao, C.H.Lin, P.K.Fu, T.P.Ko, Y.Chen.

ABSTRACT

The bifunctional enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) plays a key role in sialic acid production. It is different from the non-hydrolyzing enzymes for bacterial cell wall biosynthesis, and it is feed-back inhibited by the downstream product CMP-Neu5Ac. Here the complex crystal structure of the N-terminal epimerase part of human GNE shows a tetramer in which UDP binds to the active site and CMP-Neu5Ac binds to the dimer-dimer interface. The enzyme is locked in a tightly closed conformation. By comparing the UDP-binding modes of the non-hydrolyzing and hydrolyzing UDP-GlcNAc epimerases, we propose a possible explanation for the mechanistic difference. While the epimerization reactions of both enzymes are similar, Arg113 and Ser302 of GNE are likely involved in product hydrolysis. On the other hand, the CMP-Neu5Ac binding mode clearly elucidates why mutations in Arg263 and Arg266 can cause sialuria. Moreover, full-length modelling suggests a channel for ManNAc trafficking within the bifunctional enzyme.