7MFT

Glutamate synthase, glutamate dehydrogenase counter-enzyme complex (GudB6-GltA6-GltB6)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis.

Jayaraman, V.Lee, D.J.Elad, N.Vimer, S.Sharon, M.Fraser, J.S.Tawfik, D.S.

(2022) Nat Chem Biol 18: 161-170

  • DOI: https://doi.org/10.1038/s41589-021-00919-y
  • Primary Citation of Related Structures:  
    7MFM, 7MFT

  • PubMed Abstract: 

    Multi-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from Bacillus subtilis composed of two enzymes catalyzing opposite ('counter-enzymes') rather than sequential reactions: glutamate synthase (GltAB) and glutamate dehydrogenase (GudB), which make and break glutamate, respectively. In vivo and in vitro studies show that the primary role of complex formation is to inhibit the activity of GudB. Using cryo-electron microscopy, we elucidated the structure of the complex and the molecular basis of inhibition of GudB by GltAB. The complex exhibits unusual oscillatory progress curves and is necessary for both planktonic growth, in glutamate-limiting conditions, and for biofilm growth, in glutamate-rich media. The regulation of a key metabolic enzyme by complexing with its counter enzyme may thus enable cell growth under fluctuating glutamate concentrations.


  • Organizational Affiliation

    Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel. vijay.jayaraman@weizmann.ac.il.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate dehydrogenase424Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10Mutation(s): 0 
Gene Names: gudBB4122_2172ETA10_11605ETK61_12750GII81_12565SC09_Contig24orf00413
UniProt
Find proteins for P50735 (Bacillus subtilis (strain 168))
Explore P50735 
Go to UniProtKB:  P50735
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50735
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate synthase (NADPH) large chainB [auth G]1,520Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10Mutation(s): 0 
Gene Names: B4417_0011
UniProt
Find proteins for P39812 (Bacillus subtilis (strain 168))
Explore P39812 
Go to UniProtKB:  P39812
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39812
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate synthase (NADPH) small chainC [auth I]524Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10Mutation(s): 1 
Gene Names: B4417_0010
UniProt
Find proteins for O34399 (Bacillus subtilis (strain 168))
Explore O34399 
Go to UniProtKB:  O34399
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34399
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
F [auth I]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
D [auth G]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
G [auth I],
H [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

Download Ideal Coordinates CCD File 
E [auth G]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE1.1.0
MODEL REFINEMENTPHENIX1.19.1-4122
MODEL REFINEMENTCoot0.9.3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael2575/20
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM123159

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-05
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-05-29
    Changes: Data collection, Refinement description