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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate dehydrogenaseA424Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10Mutation(s): 0 
Gene Names: gudBB4122_2172ETA10_11605ETK61_12750GII81_12565SC09_Contig24orf00413
UniProt
Find proteins for A0A0C3GZC9 (Bacillus subtilis)
Explore A0A0C3GZC9 
Go to UniProtKB:  A0A0C3GZC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0C3GZC9
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate synthase (NADPH) large chainB [auth G]1520Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10Mutation(s): 0 
Gene Names: B4417_0011
UniProt
Find proteins for A0A164XVV7 (Bacillus subtilis)
Explore A0A164XVV7 
Go to UniProtKB:  A0A164XVV7
Entity Groups  
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UniProt GroupA0A164XVV7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence 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 A0A164XVU4 (Bacillus subtilis)
Explore A0A164XVU4 
Go to UniProtKB:  A0A164XVU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A164XVU4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / 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
 Ligand Interaction
FMN
Query on FMN

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D [auth G]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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G [auth I],
H [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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E [auth G]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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