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Basic information

Entry
Database: EMDB / ID: EMD-23825
TitleGlutamate synthase, glutamate dehydrogenase counter-enzyme complex (GudB6-GltA6-GltB6)
Map dataSingle GudB-GltAB asymmetric unit from GudB6-GltA6B6 complex
Sample
  • Complex: GudB-GltA-GltB
    • Protein or peptide: Glutamate dehydrogenase
    • Protein or peptide: Glutamate synthase (NADPH) large chain
    • Protein or peptide: Glutamate synthase (NADPH) small chain
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FE3-S4 CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: IRON/SULFUR CLUSTER
KeywordsCounter-enzyme complex / glutamate synthase / glutamate dehydrogenae / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


glutamate synthase activity / oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / glutamate biosynthetic process / glutamate dehydrogenase (NAD+) activity / amino acid metabolic process / 3 iron, 4 sulfur cluster binding / glutamine metabolic process / iron-sulfur cluster binding / nucleotide binding / metal ion binding
Similarity search - Function
Glutamate synthase, NADH/NADPH, small subunit 1 / Glutamate synthase domain / Glutamate synthase, central-N / Glutamine amidotransferases class-II / Conserved region in glutamate synthase / Glutamate synthase central domain / Glutamate synthase, alpha subunit, C-terminal / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Dihydroprymidine dehydrogenase domain II ...Glutamate synthase, NADH/NADPH, small subunit 1 / Glutamate synthase domain / Glutamate synthase, central-N / Glutamine amidotransferases class-II / Conserved region in glutamate synthase / Glutamate synthase central domain / Glutamate synthase, alpha subunit, C-terminal / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Glutamate dehydrogenase / Alpha-helical ferredoxin / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Nucleophile aminohydrolases, N-terminal / FAD/NAD(P)-binding domain superfamily / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glutamate dehydrogenase / Glutamate synthase (NADPH) small chain / Glutamate synthase (NADPH) large chain
Similarity search - Component
Biological speciesBacillus subtilis (bacteria) / Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJayaraman V / Lee DJ
Funding support Israel, United States, 2 items
OrganizationGrant numberCountry
Israel Science Foundation2575/20 Israel
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123159 United States
CitationJournal: Nat Chem Biol / Year: 2022
Title: A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis.
Authors: Vijay Jayaraman / D John Lee / Nadav Elad / Shay Vimer / Michal Sharon / James S Fraser / Dan S Tawfik /
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 ...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.
History
DepositionApr 11, 2021-
Header (metadata) releaseJan 5, 2022-
Map releaseJan 5, 2022-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mft
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23825.png

Downloads & links

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Map

FileDownload / File: emd_23825.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle GudB-GltAB asymmetric unit from GudB6-GltA6B6 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 260 pix.
= 214.24 Å		0.82 Å/pix.
x 260 pix.
= 214.24 Å		0.82 Å/pix.
x 260 pix.
= 214.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.2259822 - 1.9452305
Average (Standard dev.)0.021682033 (±0.06681354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin65170165
Dimensions260260260
Spacing260260260
CellA=B=C: 214.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8240.8240.824
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z214.240214.240214.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS17065165
NC/NR/NS260260260
D min/max/mean-0.2261.9450.022

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Supplemental data

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Mask #1

Fileemd_23825_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Single GudB-GltAB asymmetric unit from GudB6-GltA6B6 complex. Sharpen...

Fileemd_23825_additional_1.map
AnnotationSingle GudB-GltAB asymmetric unit from GudB6-GltA6B6 complex. Sharpen map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Single GudB-GltAB asymmetric unit from GudB6-GltA6B6 complex

Fileemd_23825_half_map_1.map
AnnotationSingle GudB-GltAB asymmetric unit from GudB6-GltA6B6 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Single GudB-GltAB asymmetric unit from GudB6-GltA6B6 complex

Fileemd_23825_half_map_2.map
AnnotationSingle GudB-GltAB asymmetric unit from GudB6-GltA6B6 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GudB-GltA-GltB

EntireName: GudB-GltA-GltB
Components
  • Complex: GudB-GltA-GltB
    • Protein or peptide: Glutamate dehydrogenase
    • Protein or peptide: Glutamate synthase (NADPH) large chain
    • Protein or peptide: Glutamate synthase (NADPH) small chain
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FE3-S4 CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: GudB-GltA-GltB

SupramoleculeName: GudB-GltA-GltB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Asymmetric unit (GudB-GltA-GltB) from a full GudB6-GltA6-GltB6 complex.
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 1.62 MDa

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Macromolecule #1: Glutamate dehydrogenase

MacromoleculeName: Glutamate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 (bacteria)
Molecular weightTheoretical: 47.100715 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MAADRNTGHT EEDKLDVLKS TQTVIHKALE KLGYPEEVYE LLKEPMRLLT VKIPVRMDDG SVKIFTGYRA QHNDSVGPTK GGIRFHPNV TEKEVKALSI WMSLKCGIID LPYGGGKGGI VCDPRDMSFR ELERLSRGYV RAISQIVGPT KDVPAPDVFT N SQIMAWMM ...String:
MAADRNTGHT EEDKLDVLKS TQTVIHKALE KLGYPEEVYE LLKEPMRLLT VKIPVRMDDG SVKIFTGYRA QHNDSVGPTK GGIRFHPNV TEKEVKALSI WMSLKCGIID LPYGGGKGGI VCDPRDMSFR ELERLSRGYV RAISQIVGPT KDVPAPDVFT N SQIMAWMM DEYSRIDEFN SPGFITGKPL VLGGSHGRES ATAKGVTICI KEAAKKRGID IKGARVVVQG FGNAGSYLAK FM HDAGAKV VGISDAYGGL YDPEGLDIDY LLDRRDSFGT VTKLFNDTIT NQELLELDCD ILVPAAIENQ ITEENAHNIR AKI VVEAAN GPTTLEGTKI LSDRDILLVP DVLASAGGVT VSYFEWVQNN QGFYWSEEEV EEKLEKMMVK SFNNIYEMAN NRRI DMRLA AYMVGVRKMA EASRFRGWI

UniProtKB: Glutamate dehydrogenase

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Macromolecule #2: Glutamate synthase (NADPH) large chain

MacromoleculeName: Glutamate synthase (NADPH) large chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 (bacteria)
Molecular weightTheoretical: 169.006375 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MTYNQMPKAQ GLYRPEFEHD ACGIGLYAHL KGKQTHDIVK QGLKMLCQLD HRGGQGSDPD TGDGAGLLVQ IPDAFFRKEC KNINLPEKE RYGVGMVFFS QKEDERKKIE KQINALIEQE GQVVLGWRTV PVNVGKIGTV AQKSCPFVRQ VFIGASSDLK D NLSFERKL ...String:
MTYNQMPKAQ GLYRPEFEHD ACGIGLYAHL KGKQTHDIVK QGLKMLCQLD HRGGQGSDPD TGDGAGLLVQ IPDAFFRKEC KNINLPEKE RYGVGMVFFS QKEDERKKIE KQINALIEQE GQVVLGWRTV PVNVGKIGTV AQKSCPFVRQ VFIGASSDLK D NLSFERKL YVIRKQAENW GVTEGLDFYF ASLSSQTIVY KGLLTPEQVD AFYSDLQDEA FVSAFALVHS RFSTNTFPTW ER AHPNRYL VHNGEINTLR GNINWMRARE QQFVSESFGE DLNKILPILN ADGSDSSILD NAFEFFVMAG RKPAHTAMML IPE PWTENT HMSKEKRAFY EYHSSLMEPW DGPTAISFTD GKQIGAILDR NGLRPARYYV TKDDYIIFSS EVGVIEVEQE NVLY KNRLE PGKMLLIDLE EGRIISDEEV KTQIATEYPY QKWLEEELVQ VNPDPESREE EQFSDLLTRQ KAFGYTYEDI QKYLI PVIK EGKDPLGSMG NDAPLAVLSD RAQSLFNYFK QLFAQVTNPP IDAIREQLVT STMTWLGAEG DLLHPSERNV RRIKLY TPV LSNEQFYALK TIVHPDLKSQ KIDVLFSEDL ERGLKDMFTQ AEKAISQGVS LLILSDKKMN ERLTPIPPLL AVSALHQ HL IRKGLRTKVS IIVESGEARE VHHFAALIGY GADAINPYLA YATYKQEIDE GRLDISYEEA VSKYGKSITE GVVKVMSK M GISTVQSYRG AQIFEAVGIS RDVIDRYFSG TASQLGGIDL QTIAEEAQRR HREAYQDDYS KTLEPGSDFQ WRNGGEHHA FNPKTIHTLQ WACRRNDYNL FKQYTKAADE ERIGFLRNLF AFDGNRKPLK LEEVESAESI VKRFKTGAMS FGSLSKEAHE ALAIAMNRL GGKSNSGEGG EDPKRFVPDE NGDDRRSAIK QIASGRFGVK SHYLVNADEL QIKMAQGAKP GEGGQLPGNK V YPWVADVR GSTPGVGLIS PPPHHDIYSI EDLAQLIHDL KNANRDARIS VKLVSKAGVG TIAAGVAKAT ADVIVISGYD GG TGASPKT SIKHTGLPWE LGLAEAHQTL MLNGLRDRVV LETDGKLMTG RDVVMAALLG AEEFGFATAP LVVLGCVMMR ACH LDTCPV GVATQNPELR KKFMGDPDHI VNYMLFIAEE VREYMAALGF KTFDEMIGRT DVLHVSERAK EHWKASQLDL STLL YQPEG VRTFQSPQNH KIDQSLDITT ILPAVQEAIE SGKEADISIE INNTNRVAGT ITGSEISKRY GEEGLPEDTI KLHFT GSAG QSFGAFVPKG MTLYLDGDSN DYVGKGLSGG KIIVKSSEGF NSASDDNVII GNVAFYGATS GEAYINGRAG ERFAVR NSG VNVVVEGIGD HGCEYMTGGS VVVLGDVGKN FAAGMSGGIA YVLTEDVKAF KRKCNLEMIL FESLEDEKEI QQIKAML ER HTAYTNSQKA EDLLDQWEDS VKKFVKVIPK NYKQMLASIE EQKAAGLSDE EAIMFAFEAN TKPKQNTAAS GQKQAVVQ

UniProtKB: Glutamate synthase (NADPH) large chain

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Macromolecule #3: Glutamate synthase (NADPH) small chain

MacromoleculeName: Glutamate synthase (NADPH) small chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 (bacteria)
Molecular weightTheoretical: 58.010598 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MGKPTGFMEI KREKPAERDP LTRLKDWKEY SAPFSEEASK RQGARCMDCG TPFCQIGADI NGFTSGCPIY NLIPEWNGLV YRGRWKEAL ERLLKTNNFP EFTGRVCPAP CEGSCTLAIS DPAVSIKNIE RTIIDKGFEN GWIQPRIPKK RTGKKVAIVG S GPAGLASA ...String:
MGKPTGFMEI KREKPAERDP LTRLKDWKEY SAPFSEEASK RQGARCMDCG TPFCQIGADI NGFTSGCPIY NLIPEWNGLV YRGRWKEAL ERLLKTNNFP EFTGRVCPAP CEGSCTLAIS DPAVSIKNIE RTIIDKGFEN GWIQPRIPKK RTGKKVAIVG S GPAGLASA DQLNQAGHSV TVFERADRAG GLLTYGIPNM KLEKGIVERR IKLLTQEGID FVTNTEIGVD ITADELKEQF DA VILCTGA QKQRDLLIEG RDSKGVHYAM DYLTLATKSY LDSNFKDKQF IDAKGKDVIV IGGGDTGADC VATALRQKAK SVH QFGKHP KLPPARTNDN MWPEQPHVFT LEYAYEEAEA KFGRDPREYS IQTTKMVADK NGKLKELHTI QMEKVKNEHG KYEF RELPG TEKVWPAQLV FIAIGFEGTE QPLLKQFGVN SVNNKISAAY GDYQTNIDGV FAAGDARRGQ SLIVWAINEG REVAR EVDR YLMGSSVLPG SWSHPQFEKG GGSGGGSGGS AWSHPQFENK

UniProtKB: Glutamate synthase (NADPH) small chain

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Macromolecule #4: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #5: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #6: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 6 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 60487
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11878
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3k8z

chain_id: C, residue_range: 17-424, source_name: PDB, initial_model_type: experimental model

1ofd

chain_id: A, source_name: PDB, initial_model_type: experimental model

6s6t

chain_id: G, source_name: PDB, initial_model_type: experimental model
DetailsReal-space refinement involved iterative rounds of ISOLDE, Coot and PHENIX refinement. 1OFD and 6S6T were used as templates for homology modeling in SWISS-MODEL.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7mft:
Glutamate synthase, glutamate dehydrogenase counter-enzyme complex (GudB6-GltA6-GltB6)

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