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- PDB-9i4z: Crystal structure of Thomasclavelia ramosa IgA peptidase (IgAse) ... -

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Basic information

Entry
Database: PDB / ID: 9i4z
TitleCrystal structure of Thomasclavelia ramosa IgA peptidase (IgAse) active site mutant (E330-N876)
ComponentsIgA protease
KeywordsHYDROLASE / Protease / Metallopeptidase / Metzincin
Function / homology
Function and homology information


cellulose catabolic process / metallopeptidase activity / proteolysis / extracellular region / membrane
Similarity search - Function
Domain of unknown function DUF6273 / Domain of unknown function (DUF6273) / Peptidase M64, IgA / IgA Peptidase M64 / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Metallopeptidase, catalytic domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
FORMIC ACID / IgA protease
Similarity search - Component
Biological speciesThomasclavelia ramosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRamirez-Larrota, J.S. / Eckhard, U. / Gomis-Ruth, F.X.
Funding support Spain, 3items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PRE2020-096731 Spain
Agencia Estatal de Investigacion (AEI)PID2019-107725RB-I00 Spain
Agencia Estatal de Investigacion (AEI)RYC2020-029773-I Spain
CitationJournal: PLoS Pathog / Year: 2025
Title: Biochemical and structural characterization of the human gut microbiome metallopeptidase IgAse provides insight into its unique specificity for the Fab' region of IgA1 and IgA2.
Authors: Juan Sebastián Ramírez-Larrota / Pauline Juyoux / Pablo Guerra / Ulrich Eckhard / F Xavier Gomis-Rüth /
Abstract: Human immunoglobulin A (IgA), comprising the isotypes IgA1 and IgA2, protects ~400 m2 of mucosal surfaces against microbial infections but can also lead to aberrant IgA deposits that cause disease. ...Human immunoglobulin A (IgA), comprising the isotypes IgA1 and IgA2, protects ~400 m2 of mucosal surfaces against microbial infections but can also lead to aberrant IgA deposits that cause disease. Certain bacteria have evolved peptidases that cleave the hinge between the Fab and Fc fragments of IgA, undermining its immune function. These peptidases specifically target IgA1, but not IgA2, which predominates in the gut and possesses a structurally distinct hinge region. The only known IgA2-specific peptidase is IgAse from the gut microbiome member Thomasclavelia ramosa, which also targets IgA1 but no other proteins. IgAse is a ~ 140-kDa, seven-domain, membrane-bound metallopeptidase (MP). Differential scanning fluorimetry, small-angle X-ray scattering, AI-based structural predictions, mass spectrometry, and high-resolution crystallography and cryo-electron microscopy of multidomain fragments of IgAse revealed a novel 313-residue catalytic domain (CD) from the igalysin family within the metzincin MP clan. The CD is flanked by an N-terminal globular C-type lectin-like domain and a wrapping domain (WD), followed by four all-β domains. Functional studies involving a comprehensive set of constructs (wild-type and mutant), authentic and recombinant IgA fragments, and inhibitors demonstrated that the minimal functional assembly requires the CD and WD, along with the Fab and hinge region (Fab'). Modelling studies suggested that the Fab heavy-chain constant domain interacts with the N-terminal subdomain of the CD, positioning the hinge peptide for cleavage-a mechanism confirmed by mutational analysis. These findings open avenues for therapeutic strategies to inhibit the only known IgA1/IgA2 peptidase and to develop it for dissolving pathologic IgA deposits.
History
DepositionJan 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.0Jul 23, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_refine_tls.method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgA protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,75413
Polymers63,8861
Non-polymers86812
Water7,746430
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-12 kcal/mol
Surface area22690 Å2
Unit cell
Length a, b, c (Å)46.15, 87.83, 67.47
Angle α, β, γ (deg.)90, 96.11, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein IgA protease


Mass: 63885.918 Da / Num. of mol.: 1 / Mutation: E540A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thomasclavelia ramosa (bacteria) / Gene: iga / Plasmid: pCri7b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9AES2

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Non-polymers , 5 types, 442 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350, sodium fluoride / PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 19, 2023
Details: KB mirrors (VFM and HFM in Kirkpatrick-Baez configuration)
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→45.9 Å / Num. obs: 53460 / % possible obs: 99.1 % / Redundancy: 6.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.083 / Net I/σ(I): 13.3
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.563 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 8622 / CC1/2: 0.458 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
SHELXEmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.89 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 701 -RANDOM
Rwork0.1779 ---
obs0.1784 53460 99.2 %-
Displacement parametersBiso mean: 36.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.7847 Å20 Å20.03 Å2
2---2.1139 Å20 Å2
3---2.8987 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.75→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4409 0 50 430 4889
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094583HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.886198HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2098SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes784HARMONIC5
X-RAY DIFFRACTIONt_it4583HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion586SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance9HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4206SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion2.55
LS refinement shellResolution: 1.75→1.77 Å
RfactorNum. reflection% reflection
Rfree0.4429 27 -
Rwork0.3605 --
obs0.3619 1528 87.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5138-0.0851-0.12730.4550.12420.5046-0.01660.030.04640.030.03670.04520.04640.0452-0.0201-0.0202-0.0039-0.0123-0.03020.0092-0.001923.72436.77931.1869
20.92890.05890.14440.9083-0.22351.63840.0108-0.144-0.232-0.144-0.06880.1766-0.2320.17660.0580.0076-0.02340.0113-0.00060.0154-0.092434.229246.2032-28.8892
31.88820.0783-1.10350.5851-0.3141.4614-0.0217-0.1261-0.071-0.12610.1053-0.0879-0.071-0.0879-0.0836-0.0223-0.0098-0.0321-0.06760.00470.05339.778957.7376-5.845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|330 - A|632 A|1001 - A|1001 A|1002 - A|1002 }A330 - 632
2X-RAY DIFFRACTION1{ A|330 - A|632 A|1001 - A|1001 A|1002 - A|1002 }A1001
3X-RAY DIFFRACTION1{ A|330 - A|632 A|1001 - A|1001 A|1002 - A|1002 }A1002
4X-RAY DIFFRACTION2{ A|633 - A|807 }A633 - 807
5X-RAY DIFFRACTION3{ A|808 - A|876 A|901 - A|901 }A808 - 876
6X-RAY DIFFRACTION3{ A|808 - A|876 A|901 - A|901 }A901

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