4UFB

Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with Lys-Pro

PDB DOI: https://doi.org/10.2210/pdb4UFB/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2015-03-16 Released: 2015-10-07
Deposition Author(s): Masuyer, G., Douglas, R.G., Sturrock, E.D., Acharya, K.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.235
R-Value Work: 0.207
R-Value Observed: 0.208

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structural Basis of Ac-Sdkp Hydrolysis by Angiotensin-I Converting Enzyme

Masuyer, G., Douglas, R.G., Sturrock, E.D., Acharya, K.R.

(2015) Sci Rep 5: 13742

PubMed: 26403559 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/srep13742
Primary Citation of Related Structures:
4UFA, 4UFB

PubMed Abstract:
Angiotensin-I converting enzyme (ACE) is a zinc dipeptidylcarboxypeptidase with two active domains and plays a key role in the regulation of blood pressure and electrolyte homeostasis, making it the principal target in the treatment of cardiovascular disease. More recently, the tetrapetide N-acetyl-Ser-Asp-Lys-Pro (Ac-SDKP) has emerged as a potent antifibrotic agent and negative regulator of haematopoietic stem cell differentiation which is processed exclusively by ACE. Here we provide a detailed biochemical and structural basis for the domain preference of Ac-SDKP. The high resolution crystal structures of N-domain ACE in complex with the dipeptide products of Ac-SDKP cleavage were obtained and offered a template to model the mechanism of substrate recognition of the enzyme. A comprehensive kinetic study of Ac-SDKP and domain co-operation was performed and indicated domain interactions affecting processing of the tetrapeptide substrate. Our results further illustrate the molecular basis for N-domain selectivity and should help design novel ACE inhibitors and Ac-SDKP analogues that could be used in the treatment of fibrosis disorders.

Organizational Affiliation

Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK.

Macromolecule Content

Total Structure Weight: 300.44 kDa
Atom Count: 22,065
Modelled Residue Count: 2,424
Deposited Residue Count: 2,516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANGIOTENSIN-CONVERTING ENZYME	A, B, C, D	629	Homo sapiens	Mutation(s): 8 EC: 3.4.15.1
UniProt & NIH Common Fund Data Resources
Find proteins for P12821 (Homo sapiens) Explore P12821 Go to UniProtKB: P12821
PHAROS: P12821 GTEx: ENSG00000159640
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12821
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P12821-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, K, N	2		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain K Focus chain N Interactions & Density Focus chain E Focus chain H Focus chain K Focus chain N
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, I, L, O	2		N-Glycosylation	Interactions Focus chain F Focus chain I Focus chain L Focus chain O Interactions & Density Focus chain F Focus chain I Focus chain L Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, J	3		N-Glycosylation	Interactions Focus chain G Focus chain J Interactions & Density Focus chain G Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	M, P	4		N-Glycosylation	Interactions Focus chain M Focus chain P Interactions & Density Focus chain M Focus chain P
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain OA [auth C] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain FA [auth B] SDF format, chain W [auth A] SDF format, chain Y [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A]	FA [auth B] OA [auth C] UA [auth D] VA [auth D] W [auth A] FA [auth B], OA [auth C], UA [auth D], VA [auth D], W [auth A], Y [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain OA [auth C] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth A] Focus chain Y [auth A] Interactions & Density Focus chain FA [auth B] Focus chain OA [auth C] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth A] Focus chain Y [auth A]
LYS Query on LYS Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain Z [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain Z [auth B]	IA [auth C], PA [auth D], Q [auth A], Z [auth B]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain IA [auth C] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain Z [auth B] Interactions & Density Focus chain IA [auth C] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain Z [auth B]
PRO Query on PRO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain JA [auth C] SDF format, chain QA [auth D] SDF format, chain R [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth A]	AA [auth B], JA [auth C], QA [auth D], R [auth A]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain AA [auth B] Focus chain JA [auth C] Focus chain QA [auth D] Focus chain R [auth A] Interactions & Density Focus chain AA [auth B] Focus chain JA [auth C] Focus chain QA [auth D] Focus chain R [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain GA [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth A] SDF format, chain HA [auth B] SDF format, chain MA [auth C] SDF format, chain NA [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain X [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C]	DA [auth B] EA [auth B] GA [auth B] HA [auth B] MA [auth C] DA [auth B], EA [auth B], GA [auth B], HA [auth B], MA [auth C], NA [auth C], TA [auth D], U [auth A], V [auth A], X [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain TA [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain TA [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain RA [auth D] SDF format, chain S [auth A] SDF format, chain KA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain KA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain KA [auth C]	BA [auth B], KA [auth C], RA [auth D], S [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain KA [auth C] Focus chain RA [auth D] Focus chain S [auth A] Interactions & Density Focus chain BA [auth B] Focus chain KA [auth C] Focus chain RA [auth D] Focus chain S [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain LA [auth C] SDF format, chain SA [auth D] SDF format, chain T [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain LA [auth C] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth A]	CA [auth B], LA [auth C], SA [auth D], T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain LA [auth C] Focus chain SA [auth D] Focus chain T [auth A] Interactions & Density Focus chain CA [auth B] Focus chain LA [auth C] Focus chain SA [auth D] Focus chain T [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
PRO	BindingDB: 4UFB	Ki: 8.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.235
R-Value Work: 0.207
R-Value Observed: 0.208
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.48	α = 85.46
b = 101.59	β = 85.9
c = 114.51	γ = 81.62

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-10-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-07
Type: Initial release
Version 1.1: 2018-06-20
Changes: Advisory, Data collection, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary