7XRJ | pdb_00007xrj

crystal structure of N-acetyltransferase DgcN-25328

• PDB DOI: https://doi.org/10.2210/pdb7XRJ/pdb

• Classification: TRANSFERASE
• Organism(s): Tritonibacter scottomollicae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-05-10 Released: 2023-02-01 
• Deposition Author(s): Zhang, Y.Z., Yu, Y., Cao, H.Y., Chen, X.L., Wang, P.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea.

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.

(2023) ISME J 17: 537-548

• PubMed: 36690779 
• DOI: https://doi.org/10.1038/s41396-023-01364-6
• Primary Citation Related Structures: 
  7XRJ


• 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.

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Organizational Affiliation: 
• State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia.
School of Life Sciences, University of Warwick, Coventry, UK.
University of Chinese Academy of Sciences, Beijing, China.
State Key Laboratory of Microbial Resources, the Institute of Microbiology CAS, Beijing, China.
College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China. [e-mail].
Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. [e-mail].
Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China. [e-mail].
State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China. [e-mail].
Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. [e-mail].
State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.9 kDa 
• Atom Count: 2,829 
• Modeled Residue Count: 331 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative NAD-dependent epimerase/dehydratase family protein	A	341	Tritonibacter scottomollicae	Mutation(s): 0  Gene Names: CLV89_10851 EC: 2.3.1.312
UniProt
Find proteins for A0A2T1AE85 (Tritonibacter scottomollicae) Explore A0A2T1AE85  Go to UniProtKB:  A0A2T1AE85

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.49	α = 90
b = 130.8	β = 90
c = 131.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Zhang, Y.Z., Yu, Y., Cao, H.Y., Chen, X.L., Wang, P.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	U1706207

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-02-08
  Changes: Database references
• Version 1.2: 2023-04-05
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description