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- EMDB-13591: Structure of SidJ/CaM bound to SdeA in post-catalysis state -

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Basic information

Entry
Database: EMDB / ID: EMD-13591
TitleStructure of SidJ/CaM bound to SdeA in post-catalysis state
Map data
Sample
  • Complex: SidJ/CaM-SdeA
    • Complex: Septation initiation protein and SidJ
      • Protein or peptide: Ubiquitinating/deubiquitinating enzyme SdeA
      • Protein or peptide: Calmodulin-dependent glutamylase SidJ
    • Complex: Calmodulin
      • Protein or peptide: Calmodulin
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
KeywordsGlutamylase / Pseudokinase / phosphoribosyl / ubiquitination / Complex / LIGASE
Function / homology
Function and homology information


protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Ligases / NAD+-protein-arginine ADP-ribosyltransferase / transporter inhibitor activity / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity ...protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Ligases / NAD+-protein-arginine ADP-ribosyltransferase / transporter inhibitor activity / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of calcium ion export across plasma membrane / presynaptic endocytosis / regulation of cell communication by electrical coupling involved in cardiac conduction / calcineurin-mediated signaling / adenylate cyclase binding / protein phosphatase activator activity / protein deubiquitination / detection of calcium ion / catalytic complex / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / presynaptic cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / nucleotidyltransferase activity / cysteine-type peptidase activity / substantia nigra development / regulation of heart rate / calyx of Held / adenylate cyclase activator activity / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / response to calcium ion / G2/M transition of mitotic cell cycle / long-term synaptic potentiation / spindle pole / calcium-dependent protein binding / myelin sheath / host cell / transferase activity / vesicle / transmembrane transporter binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein ubiquitination / G protein-coupled receptor signaling pathway / nucleotide binding / calcium ion binding / centrosome / protein kinase binding / protein-containing complex / proteolysis / extracellular region / metal ion binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-2 / Ubiquitinating/deubiquitinating enzyme SdeA / Calmodulin-dependent glutamylase SidJ
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAdams M / Bhogaraju S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)European Union
Citation
Journal: Nat Commun / Year: 2021
Title: Structural basis for protein glutamylation by the Legionella pseudokinase SidJ.
Authors: Michael Adams / Rahul Sharma / Thomas Colby / Felix Weis / Ivan Matic / Sagar Bhogaraju /
Abstract: Legionella pneumophila (LP) avoids phagocytosis by secreting nearly 300 effector proteins into the host cytosol. SidE family of effectors (SdeA, SdeB, SdeC and SidE) employ phosphoribosyl ...Legionella pneumophila (LP) avoids phagocytosis by secreting nearly 300 effector proteins into the host cytosol. SidE family of effectors (SdeA, SdeB, SdeC and SidE) employ phosphoribosyl ubiquitination to target multiple host Rab GTPases and innate immune factors. To suppress the deleterious toxicity of SidE enzymes in a timely manner, LP employs a metaeffector named SidJ. Upon activation by host Calmodulin (CaM), SidJ executes an ATP-dependent glutamylation to modify the catalytic residue Glu860 in the mono-ADP-ribosyl transferase (mART) domain of SdeA. SidJ is a unique glutamylase that adopts a kinase-like fold but contains two nucleotide-binding pockets. There is a lack of consensus about the substrate recognition and catalytic mechanism of SidJ. Here, we determined the cryo-EM structure of SidJ in complex with its substrate SdeA in two different states of catalysis. Our structures reveal that both phosphodiesterase (PDE) and mART domains of SdeA make extensive contacts with SidJ. In the pre-glutamylation state structure of the SidJ-SdeA complex, adenylylated E860 of SdeA is inserted into the non-canonical (migrated) nucleotide-binding pocket of SidJ. Structure-based mutational analysis indicates that SidJ employs its migrated pocket for the glutamylation of SdeA. Finally, using mass spectrometry, we identified several transient autoAMPylation sites close to both the catalytic pockets of SidJ. Our data provide unique insights into the substrate recognition and the mechanism of protein glutamylation by the pseudokinase SidJ.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution
Authors: Adams PD / Afonine PV / Bunkoczi G / Chen VB / Davis IW / Echols N / Headd JJ / Hung L / Kapral GJ / Grosse RW / McCoy AJ / Moriarty NW / Oeffner R / Read RJ / Richardson DC / Richardson JS ...Authors: Adams PD / Afonine PV / Bunkoczi G / Chen VB / Davis IW / Echols N / Headd JJ / Hung L / Kapral GJ / Grosse RW / McCoy AJ / Moriarty NW / Oeffner R / Read RJ / Richardson DC / Richardson JS / Terwilliger TC / Zwart PH
History
DepositionSep 17, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pqe
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13591.png

Downloads & links

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Map

FileDownload / File: emd_13591.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 320 pix.
= 301.12 Å		0.94 Å/pix.
x 320 pix.
= 301.12 Å		0.94 Å/pix.
x 320 pix.
= 301.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.941 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.055
Minimum - Maximum-0.23394866 - 0.4067981
Average (Standard dev.)0.00019913838 (±0.0068432777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 301.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9410.9410.941
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z301.120301.120301.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2340.4070.000

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Supplemental data

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Mask #1

Fileemd_13591_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SidJ/CaM-SdeA

EntireName: SidJ/CaM-SdeA
Components
  • Complex: SidJ/CaM-SdeA
    • Complex: Septation initiation protein and SidJ
      • Protein or peptide: Ubiquitinating/deubiquitinating enzyme SdeA
      • Protein or peptide: Calmodulin-dependent glutamylase SidJ
    • Complex: Calmodulin
      • Protein or peptide: Calmodulin
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: SidJ/CaM-SdeA

SupramoleculeName: SidJ/CaM-SdeA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Septation initiation protein and SidJ

SupramoleculeName: Septation initiation protein and SidJ / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Legionella pneumophila (bacteria)

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Supramolecule #3: Calmodulin

SupramoleculeName: Calmodulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ubiquitinating/deubiquitinating enzyme SdeA

MacromoleculeName: Ubiquitinating/deubiquitinating enzyme SdeA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 110.875203 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSAGL EVLFQGPMVG FSLYTDDTVK AAAQYAYDNY LGKPYTGSVE SAPANFGGRM VYRQHHGLSH TLRTMAYAEL IVEEARKAK LRGETLGKFK DGRTIADVTP QELKKIMIAQ AFFVAGRDDE ASDAKNYQKY HEQSRDAFLK YVKDNESTLI P DVFKDQED ...String:
HHHHHHSAGL EVLFQGPMVG FSLYTDDTVK AAAQYAYDNY LGKPYTGSVE SAPANFGGRM VYRQHHGLSH TLRTMAYAEL IVEEARKAK LRGETLGKFK DGRTIADVTP QELKKIMIAQ AFFVAGRDDE ASDAKNYQKY HEQSRDAFLK YVKDNESTLI P DVFKDQED VNFYARVIED KSHDWESTPA HVLINQGHMV DLVRVKQPPE SFLQRYFSSM QRWIGSQATE AVFGIQRQFF HA TYEVVAG FDSDNKEPHL VVSGLGRYVI GEDGQPIREA PKKGQKEGDL KVFPQTYKLK ENERLMRVDE FLKLPEIQNT FPG SGKHLQ GGMPGMNEMD YWNRLNSLNR ARCENDVDFC LKQLQTAHDK AKIEPIKQAF QSSKGKERRQ PNVDEIAAAR IIQQ ILANP DCIHDDHVLI NGQKLEQQFF RDLLAKCEMA VVGSLLNDTD IGNIDTLMRH EKDTEFHSTN PEAVPVKIGE YWIND QRIN NSSGNITQKK HDLIFLMQND AWYFSRVNAI AQNRDKGSTF KEVLITTLMT PLTSKALVDT SQAKPPTRLF RGLNLS EEF TKGLIDQANA MIANTTERLF TDHSPEAFKQ IKLNDLSKMS GRTNASTTTE IKLVKETWDS NVIFEMLDPD GLLHSKQ VG RHGEGTESEF SVYLPEDVAL VPVKVTLDGK TQKGENRYVF TFVAVKSPDF TPRHESGYAV EPFLRMQAAK LAEVKSSI E KAQRAPDLET IFNLQNEVEA VQYSHLSTGY KNFLKNTVGP VLENSLSGLM ESDTDTLSKA LAAFPSDTQW SAFNFEEAR QAKRQMDAIK QMVGNKVVLD ALTQCQDALE KQNIAGALDA LKKIPSEKEM GTIRRELREQ IQSARQELES LQRAVVTPVV TDEKKVRER YDALIENTSK KITELETGKL PNLDAVKKGI SNLSNLKQEV TVLRNEKIRM HVGTDKVDFS DVEKLEQQIQ V IDTKLADA YLLEVTKQIS A

UniProtKB: Ubiquitinating/deubiquitinating enzyme SdeA

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Macromolecule #2: Calmodulin-dependent glutamylase SidJ

MacromoleculeName: Calmodulin-dependent glutamylase SidJ / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Ligases
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 91.826992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSAGL EVLFQGPMVK QYYFARRGET STHDTSLPPP VKVLSGRSIP LKEIPFETTR NELVQIYLTS VDQLIKSNKL NSIPSQQIA SHYLFLRSLA NSETDGIKKN QILSLAKPLG IYLASKEPHV WKTINELIEK SEYPIIHYLK NNRAHSNFML A LIHEYHKE ...String:
HHHHHHSAGL EVLFQGPMVK QYYFARRGET STHDTSLPPP VKVLSGRSIP LKEIPFETTR NELVQIYLTS VDQLIKSNKL NSIPSQQIA SHYLFLRSLA NSETDGIKKN QILSLAKPLG IYLASKEPHV WKTINELIEK SEYPIIHYLK NNRAHSNFML A LIHEYHKE PLTKNQSAFV QKFRDSSVFL FPNPIYTAWL AHSYDEDSSF NPMFRERLST NFYHSTLTDN LLLRTEPKEV TL SSEHHYK KEKGPIDSSF RYQMSSDRLL RIQGRTLLFS TPQNDVVAVK VQKRGEPKST LEEEFQMADY LLKHQSRLDV YSK LPQPLG QYSVKKSEIL EISRGSLDFE RFKTLIGDSK DLEVYVYKAP LTYFTYLHDK NQDLEDLTAS VKTNVHDLFV LLRE GIMFP QLADIFHTHF GEDEREDKGR YQALVQLLNV LQFQLGRIDK WQKAVEYVNL RSSGLADLGD SLPITSLFTS SDFTK HYFS ALLTGGYHPT FFDKSSGTAN SLFTGKRRLF GNYLYLNTIA EYLLVIQLTL GSYGDKVTRD MMDKPKKEAV WRELAN VMF TSCAEAIHIM TGIPQSRALT LLKQRANIEK HFRQTQFWMT PDYSKLDEDT LQMEQYSIYS GEPEYEFTDK LVSGVGL SV DGTHQDLGGY NRESPLRELE KLLYATVTLI EGTMQLDKEF FKQLQQVEKI LSGEIKTDAN SCFEAVAQLL DLARPRCH F QKRLVLSYYE EAKLKYPSAP TDAYDSRFQV VAKTNAAITI QRFWRETRKN LSENSDIESE KPESERTTDK RLK

UniProtKB: Calmodulin-dependent glutamylase SidJ

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Macromolecule #3: Calmodulin

MacromoleculeName: Calmodulin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.066006 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHSSGL EVLFQGPHMM ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFL TMMARKMKDT DSEEEIREAF RVFDKDGNGY ISAAELRHVM TNLGEKLTDE EVDEMIREAD IDGDGQVNYE E FVQMMTAK

UniProtKB: Calmodulin-2

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58448
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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