4MWS | pdb_00004mws

Crystal structure of human PPCA (trigonal crystal form 1)

PDB DOI: https://doi.org/10.2210/pdb4MWS/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2013-09-25 Released: 2014-03-12
Deposition Author(s): Kolli, N., Garman, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.195 (Depositor), 0.197 (DCC)
R-Value Work:
0.146 (Depositor), 0.154 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Proteolytic activation of human cathepsin A.

Kolli, N., Garman, S.C.

(2014) J Biological Chem 289: 11592-11600

PubMed: 24599961 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M113.524280
Primary Citation Related Structures:
4MWS, 4MWT

PubMed Abstract:
Galactosialidosis is a human lysosomal storage disease caused by deficiency in the multifunctional lysosomal protease cathepsin A (also known as protective protein/cathepsin A, PPCA, catA, HPP, and CTSA; EC 3.4.16.5). Previous structural work on the inactive precursor human cathepsin A (zymogen) led to a two-stage model for activation, where proteolysis of a 1.6-kDa excision peptide is followed by a conformational change in a blocking peptide occluding the active site. Here we present evidence for an alternate model of activation of human cathepsin A, needing only cleavage of a 3.3-kDa excision peptide to yield full enzymatic activity, with no conformational change required. We present x-ray crystallographic, mass spectrometric, amino acid sequencing, enzymatic, and cellular data to support the cleavage-only activation model. The results clarify a longstanding question about the mechanism of cathepsin A activation and point to new avenues for the design of mechanism-based inhibitors of the enzyme.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003; Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts 01003.

Macromolecule Content

Total Structure Weight: 99.57 kDa
Atom Count: 6,749
Modeled Residue Count: 826
Deposited Residue Count: 856
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysosomal protective protein	A, B	428	Homo sapiens	Mutation(s): 0 Gene Names: CTSA, PPGB EC: 3.4.16.5
UniProt & NIH Common Fund Data Resources
Find proteins for P10619 (Homo sapiens) Explore P10619 Go to UniProtKB: P10619
PHAROS: P10619 GTEx: ENSG00000064601
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10619
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P10619-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G17689EW GlyCosmos: G17689EW GlyGen: G17689EW

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G18638YB GlyCosmos: G18638YB GlyGen: G18638YB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.195 (Depositor), 0.197 (DCC)
R-Value Work: 0.146 (Depositor), 0.154 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.889	α = 90
b = 134.889	β = 90
c = 99.805	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-03-12

Deposition Author(s):

Kolli, N.

Garman, S.C.

Revision History (Full details and data files)

Version 1.0: 2014-03-12
Type: Initial release
Version 1.1: 2015-04-15
Changes: Database references
Version 1.2: 2017-08-23
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary