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

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Basic information

Entry
Database: PDB / ID: 4ziu
TitleCrystal structure of native alpha-2-macroglobulin from Escherichia coli spanning the residues from domain MG7 to the C-terminus.
ComponentsUncharacterized lipoprotein YfhM
KeywordsMEMBRANE PROTEIN/INHIBITOR / Bacterial pan-proteinase inhibitor / membrane protein and inhibitor complex / MEMBRANE PROTEIN-INHIBITOR complex
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
NICKEL (II) ION / Alpha-2-macroglobulin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 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 28, 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 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_struct_special_symmetry ...pdbx_data_processing_status / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized lipoprotein YfhM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1968
Polymers69,6191
Non-polymers5787
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-15 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.720, 136.190, 172.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1707-

GOL

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Components

#1: Protein Uncharacterized lipoprotein YfhM / alpha-2-Macroglobulin


Mass: 69618.523 Da / Num. of mol.: 1 / Fragment: UNP residues 1018-1653
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: yfhM, b2520, JW2504 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76578
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.66 Å3/Da / Density % sol: 66.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 20% [w/v] PEG4,000, 10% isopropanol 100mM Tris-HCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALBA XALOC10.9763, 0.9788
SYNCHROTRONESRF ID2920.9763, 0.9788
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 9, 2013
DECTRIS PILATUS 6M2PIXELNov 3, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.97881
ReflectionResolution: 2.7→48 Å / Num. all: 28350 / Num. obs: 28350 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 86 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.3
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.9 / % possible all: 95.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
Cootmodel building
BUSTER2.11.5refinement
RefinementMethod to determine structure: SIRAS
Starting model: dataset of a Se-Met crystal collected at the selenium absorption peak and a native dataset to higher resolution

Resolution: 2.7→47.98 Å / Cor.coef. Fo:Fc: 0.9405 / Cor.coef. Fo:Fc free: 0.8812 / SU R Cruickshank DPI: 0.404 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.398 / SU Rfree Blow DPI: 0.268 / SU Rfree Cruickshank DPI: 0.273
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 747 2.64 %RANDOM
Rwork0.1903 ---
obs0.1916 28349 99.44 %-
Displacement parametersBiso mean: 80.34 Å2
Baniso -1Baniso -2Baniso -3
1--18.4778 Å20 Å20 Å2
2--11.2781 Å20 Å2
3---7.1997 Å2
Refine analyzeLuzzati coordinate error obs: 0.429 Å
Refinement stepCycle: 1 / Resolution: 2.7→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 32 96 5048
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015044HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.166860HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2343SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes725HARMONIC5
X-RAY DIFFRACTIONt_it5044HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion3.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion649SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5459SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3203 74 2.59 %
Rwork0.2582 2783 -
all0.2598 2857 -
obs--99.44 %
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)
14.85011.95390.71111.66230.85262.5935-0.17530.07390.34340.11770.16480.2889-0.0609-0.08630.0105-0.0314-0.0997-0.0522-0.0054-0.04410.030915.699111.02436.6796
23.87160.32670.08996.5698-0.14321.8038-0.04850.3651-0.0071-0.30610.30280.5768-0.0254-0.5194-0.2543-0.133-0.0014-0.16270.22740.1209-0.046715.584754.134255.0189
31.9666-0.36031.62421.6187-0.44464.8131-0.0713-0.347-0.10980.02190.22780.37020.0686-0.8278-0.1565-0.17080.0126-0.00050.25120.0843-0.098121.629438.708580.7382
41.97380.70630.84982.21391.46333.83660.00270.2627-0.43790.01570.18-0.24530.37630.4917-0.1827-0.02270.0016-0.06030.1463-0.078-0.057440.110324.179656.7411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1015 - 1125 }
2X-RAY DIFFRACTION2{A|1126 - 1170 A|1440 - 1495 }
3X-RAY DIFFRACTION3{A|1171 - 1439 }
4X-RAY DIFFRACTION4{A|1496 - 1653 }

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