7XRJ

crystal structure of N-acetyltransferase DgcN-25328

Summary for 7XRJ

• Entry DOI: 10.2210/pdb7xrj/pdb
• Descriptor: Putative NAD-dependent epimerase/dehydratase family protein, SULFATE ION (3 entities in total)
• Functional Keywords: n-acetyltransferase, d-glu metabolism, d-glu, acetyl-coa, transferase
• Biological source: Tritonibacter scottomollicae
• Total number of polymer chains: 1
• Total formula weight: 36899.88

Authors

Zhang, Y.Z.,Yu, Y.,Cao, H.Y.,Chen, X.L.,Wang, P. (deposition date: 2022-05-10, release date: 2023-02-01, Last modification date: 2023-11-29)

Primary citation

Yu, Y.,Wang, P.,Cao, H.Y.,Teng, Z.J.,Zhu, Y.,Wang, M.,McMinn, A.,Chen, Y.,Xiang, H.,Zhang, Y.Z.,Chen, X.L.,Zhang, Y.Q.
Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea.
Isme J, 17:537-548, 2023

PubMed Abstract: D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.

PubMed: 36690779
DOI: 10.1038/s41396-023-01364-6

Experimental method

X-RAY DIFFRACTION (2.2 Å)