4HXF

Acylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethyl ketone

PDB DOI: https://doi.org/10.2210/pdb4HXF/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-09 Released: 2013-05-08
Deposition Author(s): Kiss-Szeman, A., Menyhard, D.K., Tichy-Racs, E., Hornung, B., Radi, K., Szeltner, Z., Domokos, K., Szamosi, I., Naray-Szabo, G., Polgar, L., Harmat, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 ?
R-Value Free: 0.186
R-Value Work: 0.155
R-Value Observed: 0.156

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

A Self-compartmentalizing Hexamer Serine Protease from Pyrococcus Horikoshii: SUBSTRATE SELECTION ACHIEVED THROUGH MULTIMERIZATION.

Menyhard, D.K., Kiss-Szeman, A., Tichy-Racs, E., Hornung, B., Radi, K., Szeltner, Z., Domokos, K., Szamosi, I., Naray-Szabo, G., Polgar, L., Harmat, V.

(2013) J Biol Chem 288: 17884-17894

PubMed: 23632025 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M113.451534
Primary Citation of Related Structures:
4HXE, 4HXF, 4HXG

PubMed Abstract:
Oligopeptidases impose a size limitation on their substrates, the mechanism of which has long been under debate. Here we present the structure of a hexameric serine protease, an oligopeptidase from Pyrococcus horikoshii (PhAAP), revealing a complex, self-compartmentalized inner space, where substrates may access the monomer active sites passing through a double-gated "check-in" system, first passing through a pore on the hexamer surface and then turning to enter through an even smaller opening at the monomers' domain interface. This substrate screening strategy is unique within the family. We found that among oligopeptidases, a residue of the catalytic apparatus is positioned near an amylogenic β-edge, which needs to be protected to prevent aggregation, and we found that different oligopeptidases use different strategies to achieve such an end. We propose that self-assembly within the family results in characteristically different substrate selection mechanisms coupled to different multimerization states.

Organizational Affiliation

Protein Modeling Research Group, Hungarian Academy of Sciences, E?tv?s Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary.

Macromolecule Content

Total Structure Weight: 75.12 kDa
Atom Count: 5,892
Modelled Residue Count: 613
Deposited Residue Count: 622
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH0594	A [auth B]	622	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: PH0594 EC: 3.4.19.1
UniProt
Find proteins for O58323 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58323 Go to UniProtKB: O58323
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O58323
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y3A Query on Y3A Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide C₂₂ H₂₆ Cl N₃ O₅ WLEADEPGUSFGIL-OALUTQOASA-N		Interactions Focus chain B Interactions & Density Focus chain B
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain H [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain H [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	H [auth B] I [auth B] J [auth B] K [auth B] L [auth B] H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B], E [auth B], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001053 (Y3A) Query on PRD_001053	B	Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM)	Peptide-like / Enzyme inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 ?
R-Value Free: 0.186
R-Value Work: 0.155
R-Value Observed: 0.156
Space Group: H 3 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 184.057	α = 90
b = 184.057	β = 90
c = 145.529	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-05-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-08
Type: Initial release
Version 1.1: 2013-05-15
Changes: Database references
Version 1.2: 2013-07-03
Changes: Database references
Version 1.3: 2014-10-08
Changes: Non-polymer description
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.5: 2023-10-18
Changes: Structure summary
Version 1.6: 2024-03-13
Changes: Source and taxonomy
Version 1.7: 2024-11-20
Changes: Structure summary

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Help and Resources

4HXF

Acylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethyl ketone

A Self-compartmentalizing Hexamer Serine Protease from Pyrococcus Horikoshii: SUBSTRATE SELECTION ACHIEVED THROUGH MULTIMERIZATION.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)