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- PDB-4zjh: Crystal structure of native alpha-2-macroglobulin from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 4zjh
TitleCrystal structure of native alpha-2-macroglobulin from Escherichia coli spanning domains NIE-MG1.
Componentsalpha-2-Macroglobulin
KeywordsMEMBRANE PROTEIN / Bacterial pan-proteinase inhibitor
Function / homology
Function and homology information


endopeptidase inhibitor activity / protein homodimerization activity / extracellular space / plasma membrane
Similarity search - Function
Alpha-2-macroglobulin MG3 domain / Alpha-2-macroglobulin, bacteria / Alpha-2-macroglobulin, MG1 domain / Bacterial Alpha-2-macroglobulin, MG5 domain / Bacterial alpha-2-macroglobulin MG10 domain / Bacterial Alpha-2-macroglobulin, MG6 domain / : / : / Bacterial alpha-2-macroglobulin MG3 domain / Bacterial macroglobulin domain 6 ...Alpha-2-macroglobulin MG3 domain / Alpha-2-macroglobulin, bacteria / Alpha-2-macroglobulin, MG1 domain / Bacterial Alpha-2-macroglobulin, MG5 domain / Bacterial alpha-2-macroglobulin MG10 domain / Bacterial Alpha-2-macroglobulin, MG6 domain / : / : / Bacterial alpha-2-macroglobulin MG3 domain / Bacterial macroglobulin domain 6 / Bacterial Alpha-2-macroglobulin MG1 domain / Bacterial Alpha-2-macroglobulin MG5 domain / Bacterial Alpha-2-macroglobulin MG10 domain / Bacterial alpha-2 macroglobulin MG2 domain / A2MG, CUB domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ACETATE ION / Alpha-2-macroglobulin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsGarcia-Ferrer, I. / Arede, P. / Gomez-Blanco, J. / Luque, D. / Duquerroy, S. / Caston, J.R. / Goulas, T. / Gomis-Ruth, X.F.
Funding support Spain, 3items
OrganizationGrant numberCountry
European CommunityFP7-PEOPLE-2011-ITN-290246 Spain
European CommunityFP7-HEALTH-2012-306029-2 Spain
Spanish Ministry for Education, Culture and SportAP2010-3799 Spain
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition.
Authors: Irene Garcia-Ferrer / Pedro Arêde / Josué Gómez-Blanco / Daniel Luque / Stephane Duquerroy / José R Castón / Theodoros Goulas / F Xavier Gomis-Rüth /
Abstract: The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2- ...The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2-macroglobulin (α2M). Escherichia coli α2M (ECAM) is a ∼ 180-kDa multidomain membrane-anchored pan-peptidase inhibitor, which is cleaved by host endopeptidases in an accessible bait region. Structural studies by electron microscopy and crystallography reveal that this cleavage causes major structural rearrangement of more than half the 13-domain structure from a native to a compact induced form. It also exposes a reactive thioester bond, which covalently traps the peptidase. Subsequently, peptidase-laden ECAM is shed from the membrane and may dimerize. Trapped peptidases are still active except against very large substrates, so inhibition potentially prevents damage of large cell envelope components, but not host digestion. Mechanistically, these results document a novel monomeric "snap trap."
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha-2-Macroglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1283
Polymers22,9771
Non-polymers1512
Water3,603200
1


  • Idetical with deposited unit
  • defined by software
  • MONOMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint1 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.490, 32.860, 58.320
Angle α, β, γ (deg.)90.00, 102.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alpha-2-Macroglobulin /


Mass: 22976.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: yfhM, b2520, JW2504 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P76578
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% [w/v] PEG3,350 200mM ammonium acetate 100mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793, 0.9687
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.96871
ReflectionResolution: 1.6→57 Å / Num. obs: 24951 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.69 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 4.6 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
Cootmodel building
BUSTER2.11.5refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→49.34 Å / Cor.coef. Fo:Fc: 0.9548 / Cor.coef. Fo:Fc free: 0.9504 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 730 2.93 %RANDOM
Rwork0.1821 ---
obs0.1831 24939 99.51 %-
Displacement parametersBiso mean: 32.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.9082 Å20 Å22.3599 Å2
2--4.1123 Å20 Å2
3----7.0206 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.6→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 10 200 1860
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011692HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.082304HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d806SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes249HARMONIC5
X-RAY DIFFRACTIONt_it1692HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.98
X-RAY DIFFRACTIONt_other_torsion2.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion217SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2096SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2843 84 3.08 %
Rwork0.2114 2644 -
all0.2136 2728 -
obs--99.51 %
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)
11.5961.14880.04372.6129-0.12110.26320.0741-0.1545-0.07340.0762-0.14390.00550.04350.00620.06980.02550.0144-0.00170.06150.00580.068831.57272.475417.4179
21.9877-0.1778-0.35891.06540.21451.217-0.0274-0.1017-0.07890.07110.055-0.0930.01440.1015-0.0276-0.00090.0009-0.02660.00160.01390.022955.69329.77398.7705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-2 - -2 A|-1 - -1 A|163 - 291}
2X-RAY DIFFRACTION2{A|292 - 368}

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