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- PDB-8qhl: Human Angiotensin-1 converting enzyme N-domain in complex with th... -

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Basic information

Entry
Database: PDB / ID: 8qhl
TitleHuman Angiotensin-1 converting enzyme N-domain in complex with the lactotripeptide VPP
Components
  • Angiotensin-converting enzyme
  • VAL-PRO-PRO
KeywordsHYDROLASE / Angiotensin-I converting enzyme / Zinc-dependent endopeptidase / di-peptidyl carboxxypeptidase
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import / positive regulation of peptidyl-cysteine S-nitrosylation / response to laminar fluid shear stress / negative regulation of gap junction assembly / metallodipeptidase activity / positive regulation of systemic arterial blood pressure / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of glucose import / vasoconstriction / hormone metabolic process / neutrophil mediated immunity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / arachidonic acid secretion / post-transcriptional regulation of gene expression / eating behavior / heterocyclic compound binding / lung alveolus development / heart contraction / peptide catabolic process / response to dexamethasone / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / peptidyl-dipeptidase activity / hematopoietic stem cell differentiation / blood vessel remodeling / angiotensin maturation / amyloid-beta metabolic process / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / positive regulation of vasoconstriction / sperm midpiece / blood vessel diameter maintenance / response to nutrient levels / basal plasma membrane / kidney development / angiotensin-activated signaling pathway / female pregnancy / cellular response to glucose stimulus / brush border membrane / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / metallopeptidase activity / male gonad development / actin binding / peptidase activity / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / calmodulin binding / response to hypoxia / endosome / response to xenobiotic stimulus / positive regulation of apoptotic process / external side of plasma membrane / negative regulation of gene expression / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGregory, K.S. / Cozier, G.E. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X001032/1 United Kingdom
CitationJournal: Febs Lett. / Year: 2024
Title: Structural insights into the inhibitory mechanism of angiotensin-I-converting enzyme by the lactotripeptides IPP and VPP.
Authors: Gregory, K.S. / Cozier, G.E. / Schwager, S.L.U. / Sturrock, E.D. / Acharya, K.R.
History
DepositionSep 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Angiotensin-converting enzyme
D: VAL-PRO-PRO
A: Angiotensin-converting enzyme
C: VAL-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,67729
Polymers145,6094
Non-polymers5,06825
Water7,999444
1
B: Angiotensin-converting enzyme
D: VAL-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,21714
Polymers72,8052
Non-polymers2,41212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-9 kcal/mol
Surface area24670 Å2
2
A: Angiotensin-converting enzyme
C: VAL-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,46115
Polymers72,8052
Non-polymers2,65613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-37 kcal/mol
Surface area24880 Å2
Unit cell
Length a, b, c (Å)73.337, 78.222, 83.011
Angle α, β, γ (deg.)88.750, 64.703, 75.248
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 4 molecules BADC

#1: Protein Angiotensin-converting enzyme / ACE / Dipeptidyl carboxypeptidase I / Kininase II


Mass: 72493.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE, DCP, DCP1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P12821, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A
#2: Protein/peptide VAL-PRO-PRO


Mass: 311.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle)

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Sugars , 4 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 10 types, 463 molecules

#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#12: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#13: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#14: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#15: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 550 MME/PEG 20000, 0.1 M Tris/Bicine pH 8.5, and 60 mM divalent cations (molecular dimensions screen, Morpheus A9)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.9→75.27 Å / Num. obs: 123919 / % possible obs: 97.9 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rpim(I) all: 0.06 / Net I/σ(I): 7.2
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 6083 / CC1/2: 0.357 / Rpim(I) all: 0.937

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→75.268 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.056 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.137 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.233 6246 5.041 %RANDOM
Rwork0.1883 117664 --
all0.191 ---
obs-123910 97.891 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.526 Å20.365 Å20.145 Å2
2---0.333 Å20.702 Å2
3---0.606 Å2
Refinement stepCycle: LAST / Resolution: 1.9→75.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9914 0 326 445 10685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01210623
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.66914450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97451224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.413565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.249101611
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.31110530
X-RAY DIFFRACTIONr_chiral_restr0.1410.21517
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028408
X-RAY DIFFRACTIONr_nbd_refined0.220.24329
X-RAY DIFFRACTIONr_nbtor_refined0.3130.27109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2411
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.27
X-RAY DIFFRACTIONr_mcbond_it2.6662.2744890
X-RAY DIFFRACTIONr_mcangle_it3.5644.0766116
X-RAY DIFFRACTIONr_scbond_it4.2812.7515733
X-RAY DIFFRACTIONr_scangle_it5.9914.8728334
X-RAY DIFFRACTIONr_lrange_it7.40925.62915450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.3534450.33786210.33893920.9120.91796.5290.344
1.949-2.0030.3484280.32384370.32591300.9150.92697.09750.33
2.003-2.0610.3194020.29382350.29488750.9310.9497.31830.296
2.061-2.1240.2964330.26679220.26885850.9410.95197.32090.267
2.124-2.1940.2783930.24577220.24683320.950.9697.39560.242
2.194-2.2710.2753900.23275240.23481020.9510.96597.67960.224
2.271-2.3560.2573660.21972420.22177990.9570.96997.5510.212
2.356-2.4520.2613730.21169700.21375080.9560.97297.80230.202
2.452-2.5610.2753440.19966740.20371690.9520.97697.89370.189
2.561-2.6860.2673440.19164030.19568800.960.97898.06690.181
2.686-2.8310.2473530.18960560.19265170.9610.97998.34280.178
2.831-3.0030.2563170.18857860.19162000.9620.9898.43550.177
3.003-3.210.2292820.18754620.18958160.9670.9898.7620.176
3.21-3.4660.2322960.18350290.18553840.9690.98298.90420.174
3.466-3.7960.2082720.16946650.17149870.9740.98598.99740.162
3.796-4.2430.1782370.13241990.13444840.9850.99198.92950.124
4.243-4.8970.1611900.12637810.12840050.9860.99199.15110.118
4.897-5.9910.1931770.14331410.14633470.9810.98999.13360.137
5.991-8.4460.2241340.17824310.1825860.9760.98799.18790.17
8.446-75.2680.203700.17813640.17914370.980.98299.79120.159
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)
11.1728-0.19430.17091.41680.26880.70150.09030.0931-0.0735-0.095-0.03020.0290.00180.0089-0.06010.07230.05340.03130.04150.02290.03372.0098-15.0044-18.7805
20.8359-0.2249-0.09251.27660.29361.7948-0.0232-0.1222-0.01330.15580.00850.10020.029-0.09580.01480.09090.02480.06010.03750.00140.0863-1.482315.242318.9019
300000000000000-00.1471000.147100.1471000
Refinement TLS groupSelection: ALL

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