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- PDB-4ziq: Crystal structure of trypsin activated alpha-2-macroglobulin from... -

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Basic information

Entry
Database: PDB / ID: 4ziq
TitleCrystal structure of trypsin activated alpha-2-macroglobulin from Escherichia coli.
ComponentsUncharacterized lipoprotein YfhM
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
Alpha-2-macroglobulin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.55 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 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized lipoprotein YfhM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,1745
Polymers177,9761
Non-polymers1984
Water1,892105
1
A: Uncharacterized lipoprotein YfhM
hetero molecules

A: Uncharacterized lipoprotein YfhM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,34810
Polymers355,9512
Non-polymers3978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area6020 Å2
ΔGint-69 kcal/mol
Surface area121640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.280, 95.360, 81.090
Angle α, β, γ (deg.)90.00, 104.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized lipoprotein YfhM


Mass: 177975.672 Da / Num. of mol.: 1 / Fragment: UNP residues 40-1563
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 12-16% [w/v] PEG8,000 100mM Tris-HCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALBA XALOC10.9724, 0.9768, 0.9788, 0.9793, 0.9791
SYNCHROTRONESRF ID23-120.9724, 0.9768, 0.9788, 0.9793, 0.9791
SYNCHROTRONESRF ID2930.9724, 0.9768, 0.9788, 0.9793, 0.9791
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 9, 2013
DECTRIS PILATUS 6M2PIXELNov 22, 2013
DECTRIS PILATUS 6M3PIXELNov 3, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray2
3MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97241
20.97681
30.97881
40.97931
50.97911
ReflectionResolution: 2.55→47.7 Å / Num. all: 65409 / Num. obs: 65409 / % possible obs: 99.4 % / Redundancy: 14.9 % / Biso Wilson estimate: 85.37 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.3
Reflection shellResolution: 2.55→2.7 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.163 / Mean I/σ(I) obs: 2.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
Cootmodel building
BUSTER2.10.2refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.55→47.68 Å / Cor.coef. Fo:Fc: 0.9501 / Cor.coef. Fo:Fc free: 0.9346 / SU R Cruickshank DPI: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.336 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.236
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 1083 1.66 %RANDOM
Rwork0.1898 ---
obs0.1903 65374 98.97 %-
Displacement parametersBiso mean: 111.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.477 Å20 Å210.7971 Å2
2---7.0753 Å20 Å2
3---4.5982 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å
Refinement stepCycle: 1 / Resolution: 2.55→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11224 0 9 105 11338
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911461HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0515589HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5279SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes328HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1644HARMONIC5
X-RAY DIFFRACTIONt_it11461HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion3.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1462SEMIHARMONIC5
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_contact12191SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3129 76 1.7 %
Rwork0.3133 4383 -
all0.3133 4459 -
obs--91.84 %
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)
111.2886-3.7784-1.78134.258-0.39610.592-0.04160.0884-0.2282-0.07080.14820.01310.47320.271-0.10670.3988-0.2238-0.42420.14530.31790.681104.5504-12.924874.8188
26.8242.2735-1.90114.8758-2.71882.4601-0.0326-0.1497-0.17290.11970.05610.02240.28420.0009-0.02350.4697-0.3678-0.25510.1530.36680.698579.6349-12.827382.5973
34.88842.8682.25374.7296-5.38282.5392-0.0071-0.08080.03030.06390.05070.0509-0.0418-0.0323-0.04370.0571-0.2827-0.27640.06740.30170.429472.41762.913371.0874
44.04152.3881-0.89764.3949-1.14093.56410.1662-1.1017-0.57940.26060.01120.590.4058-1.1672-0.1775-0.2451-0.2060.11240.67510.31750.044761.22325.443681.0575
53.2448-1.06510.39342.81890.13381.85530.30430.416-0.5456-0.6812-0.08540.39770.1356-0.1758-0.2190.1202-0.0149-0.18240.0081-0.0495-0.064974.62325.963546.3006
66.365-0.0244-1.26174.5122-1.77666.5880.1371-0.4223-0.7672-0.253-0.3839-0.23020.37810.86110.24680.27240.0427-0.2548-0.23070.02280.604793.68764.071256.1666
74.73042.7601-0.11279.16041.25322.63710.0110.3286-0.2448-0.1480.03320.20090.39430.0469-0.04420.2396-0.526-0.25330.19980.23930.823864.5682-9.939467.2529
80.1617-0.83160.62623.20460.03161.40710.1359-0.1452-0.54650.1973-0.06580.05940.5012-0.5817-0.0701-0.0822-0.3995-0.12470.10930.34220.455667.60778.264969.1544
90.78520.6042-1.14781.93531.3291.88070.04410.05470.0920.12840.02890.1999-0.2192-0.1265-0.0730.03350.09270.04370.1469-0.0251-0.116872.626646.968577.0376
104.60442.4908-0.89813.2387-2.02663.47730.224-0.3413-0.5132-0.076-0.14250.53750.2058-1.0255-0.0815-0.3572-0.1953-0.11230.69090.2530.504643.902525.697866.9735
114.4132-0.95192.05942.6092-1.45983.0722-0.07430.03520.6033-0.12120.09380.6267-0.7269-0.8848-0.01950.19680.3526-0.14840.22930.0810.143358.400255.803155.9399
122.2095-0.75210.38043.7865-1.071210.0575-0.3505-1.10130.36170.62440.43870.2837-0.4473-0.2128-0.08820.39050.2917-0.03020.3226-0.1068-0.1580.618953.380995.7483
133.24980.847-0.80011.4729-0.12522.5989-0.03450.12990.0288-0.12220.0010.00910.0447-0.02160.0335-0.01340.07430.0523-0.0202-0.0278-0.275113.755537.8356104.2494
142.4466-0.05690.69121.49270.10914.6866-0.07990.00930.1552-0.04770.02870.0942-0.41110.22170.0512-0.1156-0.02080.012-0.07220.04-0.256486.842742.553866.3523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|166 - 289}
2X-RAY DIFFRACTION2{A|290 - 367}
3X-RAY DIFFRACTION3{A|368 - 385}
4X-RAY DIFFRACTION4{A|386 - 483}
5X-RAY DIFFRACTION5{A|484 - 611}
6X-RAY DIFFRACTION6{A|612 - 754}
7X-RAY DIFFRACTION7{A|755 - 853}
8X-RAY DIFFRACTION8{A|901 - 938}
9X-RAY DIFFRACTION9{A|949 - 966}
10X-RAY DIFFRACTION10{A|854 - 900 A|967 - 1019}
11X-RAY DIFFRACTION11{A|1020 - 1126}
12X-RAY DIFFRACTION12{A|1127 - 1170 A|1442 - 1498}
13X-RAY DIFFRACTION13{A|1171 - 1441}
14X-RAY DIFFRACTION14{A|1499 - 1653}

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