4QBB | pdb_00004qbb

Structure of the foot-and-mouth disease virus leader proteinase in complex with inhibitor (N~2~-[(3S)-4-({(2R)-1-[(4-CARBAMIMIDAMIDOBUTYL)AMINO]-4-METHYL-1-OXOPENTAN-2-YL}AMINO)-3-HYDROXY-4-OXOBUTANOYL]-L-ARGINYL-L-PROLINAMIDE)

PDB DOI: https://doi.org/10.2210/pdb4QBB/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Foot-and-mouth disease virus (strain O1)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-07 Released: 2014-11-05
Deposition Author(s): Grishkovskaya, I., Steinberger, J., Cencic, R., Juliano, M.A., Juliano, L., Skern, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.201 (Depositor), 0.201 (DCC)
R-Value Work:
0.170 (Depositor), 0.172 (DCC)
R-Value Observed:
0.171 (Depositor)

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Literature

Foot-and-mouth disease virus leader proteinase: Structural insights into the mechanism of intermolecular cleavage.

Steinberger, J., Grishkovskaya, I., Cencic, R., Juliano, L., Juliano, M.A., Skern, T.

(2014) Virology 468-470C: 397-408

PubMed: 25240326 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.virol.2014.08.023
Primary Citation Related Structures:
4QBB

PubMed Abstract:
Translation of foot-and-mouth disease virus RNA initiates at one of two start codons leading to the synthesis of two forms of leader proteinase L(pro) (Lab(pro) and Lb(pro)). These forms free themselves from the viral polyprotein by intra- and intermolecular self-processing and subsequently cleave the cellular eukaryotic initiation factor (eIF) 4 G. During infection, Lb(pro) removes six residues from its own C-terminus, generating sLb(pro). We present the structure of sLb(pro) bound to the inhibitor E64-R-P-NH2, illustrating how sLb(pro) can cleave between Lys/Gly and Gly/Arg pairs. In intermolecular cleavage on polyprotein substrates, Lb(pro) was unaffected by P1 or P1' substitutions and processed a substrate containing nine eIF4GI cleavage site residues whereas sLb(pro) failed to cleave the eIF4GI containing substrate and cleaved appreciably more slowly on mutated substrates. Introduction of 70 eIF4GI residues bearing the Lb(pro) binding site restored cleavage. These data imply that Lb(pro) and sLb(pro) may have different functions in infected cells.

Organizational Affiliation

Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria.

Macromolecule Content

Total Structure Weight: 59.14 kDa
Atom Count: 4,440
Modeled Residue Count: 472
Deposited Residue Count: 501
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leader protease	A, B, C	167	Foot-and-mouth disease virus (strain O1)	Mutation(s): 0 EC: 3.4.22.46
UniProt
Find proteins for P03305 (Foot-and-mouth disease virus serotype O) Explore P03305 Go to UniProtKB: P03305
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03305
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E69 Query on E69 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C]	N~2~-[(3S)-4-({(2R)-1-[(4-carbamimidamidobutyl)amino]-4-methyl-1-oxopentan-2-yl}amino)-3-hydroxy-4-oxobutanoyl]-L-arginyl-L-prolinamide C₂₆ H₄₉ N₁₁ O₆ WPRWGQXJPOBGDO-RDGPPVDQSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.201 (Depositor), 0.201 (DCC)
R-Value Work: 0.170 (Depositor), 0.172 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.808	α = 90
b = 110.682	β = 98.12
c = 56.774	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
REFMAC	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-11-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-05
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary