5EER

Crystal structure of DapB from Corynebacterium glutamicum

Summary for 5EER

• Entry DOI: 10.2210/pdb5eer/pdb
• Related: 5EER
• Descriptor: 4-hydroxy-tetrahydrodipicolinate reductase, SULFATE ION (3 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
• Total number of polymer chains: 1
• Total formula weight: 26108.24

Authors

Sagong, H.-Y.,Kim, K.-J. (deposition date: 2015-10-23, release date: 2015-11-11, Last modification date: 2023-11-08)

Primary citation

Sagong, H.Y.,Kim, K.J.
Structural Insight into Dihydrodipicolinate Reductase from Corybebacterium glutamicum for Lysine Biosynthesis.
J. Microbiol. Biotechnol., 26:226-232, 2016

PubMed Abstract: Dihydrodipicolinate reductase is an enzyme that converts dihydrodipicolinate to tetrahydrodipicolinate using an NAD(P)H cofactor in L-lysine biosynthesis. To increase the understanding of the molecular mechanisms of lysine biosynthesis, we determined the crystal structure of dihydrodipicolinate reductase from Corynebacterium glutamicum (CgDapB). CgDapB functions as a tetramer, and each protomer is composed of two domains, an Nterminal domain and a C-terminal domain. The N-terminal domain mainly contributes to nucleotide binding, whereas the C-terminal domain is involved in substrate binding. We elucidated the mode of cofactor binding to CgDapB by determining the crystal structure of the enzyme in complex with NADP(+) and found that CgDapB utilizes both NADH and NADPH as cofactors. Moreover, we determined the substrate binding mode of the enzyme based on the coordination mode of two sulfate ions in our structure. Compared with Mycobacterium tuberculosis DapB in complex with its cofactor and inhibitor, we propose that the domain movement for active site constitution occurs when both cofactor and substrate bind to the enzyme.

PubMed: 26502738
DOI: 10.4014/jmb.1508.08086

Experimental method

X-RAY DIFFRACTION (2.5 Å)