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- PDB-7uvl: IgA1 Protease with IgA1 substrate -

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Basic information

Entry
Database: PDB / ID: 7uvl
TitleIgA1 Protease with IgA1 substrate
Components
  • Immunoglobulin alpha-1 heavy chain
  • Immunoglobulin alpha-1 heavy constant
  • Immunoglobulin alpha-1 light chain
  • LPXTG-motif cell wall anchor domain protein
KeywordsIMMUNE SYSTEM / complex
Function / homology
Function and homology information


secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / IgA immunoglobulin complex / IgG immunoglobulin complex / positive regulation of respiratory burst / immunoglobulin complex, circulating / Scavenging of heme from plasma / immunoglobulin receptor binding ...secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / IgA immunoglobulin complex / IgG immunoglobulin complex / positive regulation of respiratory burst / immunoglobulin complex, circulating / Scavenging of heme from plasma / immunoglobulin receptor binding / serine-type peptidase activity / complement activation, classical pathway / antigen binding / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / metalloendopeptidase activity / antibacterial humoral response / adaptive immune response / blood microparticle / immune response / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / plasma membrane
Similarity search - Function
Peptidase M26, N-terminal domain / GLUG / Peptidase M26, C-terminal domain / M26 IgA1-specific Metallo-endopeptidase N-terminal region / M26 IgA1-specific Metallo-endopeptidase C-terminal region / The GLUG motif / G5 domain / G5 domain / G5 domain profile. / G5 ...Peptidase M26, N-terminal domain / GLUG / Peptidase M26, C-terminal domain / M26 IgA1-specific Metallo-endopeptidase N-terminal region / M26 IgA1-specific Metallo-endopeptidase C-terminal region / The GLUG motif / G5 domain / G5 domain / G5 domain profile. / G5 / Trypsin-like peptidase domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold
Similarity search - Domain/homology
LPXTG-motif cell wall anchor domain protein / Immunoglobulin heavy constant alpha 1
Similarity search - Component
Biological speciesGemella haemolysans (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsEisenmesser, Z.E. / Zheng, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI146295 United States
CitationJournal: Commun Biol / Year: 2022
Title: A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases.
Authors: Jasmina S Redzic / Jeremy Rahkola / Norman Tran / Todd Holyoak / Eunjeong Lee / Antonio Javier Martín-Galiano / Nancy Meyer / Hongjin Zheng / Elan Eisenmesser /
Abstract: The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by ...The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the first to describe the structures of a metal-dependent IgA1P (metallo-IgA1P) produced from Gram-positive Streptococcus pneumoniae both in the absence and presence of its IgA1 substrate through cryo-EM single particle reconstructions. This prior study revealed an active-site gating mechanism reliant on substrate-induced conformational changes to the enzyme that begged the question of whether such a mechanism is conserved among the wider Gram-positive metallo-IgA1P subfamily of virulence factors. Here, we used cryo-EM to characterize the metallo-IgA1P of a more distantly related family member from Gemella haemolysans, an emerging opportunistic pathogen implicated in meningitis, endocarditis, and more recently bacteremia in the elderly. While the substrate-free structures of these two metallo-IgA1Ps exhibit differences in the relative starting positions of the domain responsible for gating substrate, the enzymes have similar domain orientations when bound to IgA1. Together with biochemical studies that indicate these metallo-IgA1Ps have similar binding affinities and activities, these data indicate that metallo-IgA1P binding requires the specific IgA1 substrate to open the enzymes for access to their active site and thus, largely conform to an "induced fit" model.
History
DepositionMay 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: LPXTG-motif cell wall anchor domain protein
B: Immunoglobulin alpha-1 heavy constant
A: Immunoglobulin alpha-1 heavy constant
L: Immunoglobulin alpha-1 light chain
H: Immunoglobulin alpha-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)240,9545
Polymers240,9545
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein LPXTG-motif cell wall anchor domain protein


Mass: 146820.328 Da / Num. of mol.: 1 / Mutation: A942E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gemella haemolysans (bacteria) / Gene: GEMHA0001_0491 / Production host: Escherichia coli (E. coli) / References: UniProt: C5NYF3
#2: Protein Immunoglobulin alpha-1 heavy constant / Ig alpha-1 chain C region / Ig alpha-1 chain C region BUR / Ig alpha-1 chain C region TRO


Mass: 22784.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHA1 / Production host: Mus sp. (mice) / References: UniProt: P01876
#3: Antibody Immunoglobulin alpha-1 light chain


Mass: 24009.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus sp. (mice)
#4: Antibody Immunoglobulin alpha-1 heavy chain


Mass: 24554.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus sp. (mice)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: IgA1 Protease with IgA1 substrate / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Gemella haemolysans (bacteria)1379
31Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
31Mus sp. (mice)10095
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMSodium ChlorideNaClSodium chloride1
220 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidHEPES1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205808 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316842
ELECTRON MICROSCOPYf_angle_d0.53222889
ELECTRON MICROSCOPYf_dihedral_angle_d4.6482318
ELECTRON MICROSCOPYf_chiral_restr0.0412608
ELECTRON MICROSCOPYf_plane_restr0.0042965

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