6SS2

Structure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0021158


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional characterization of C0021158, a high-affinity monoclonal antibody that inhibits Arginase 2 function via a novel non-competitive mechanism of action.

Austin, M.Burschowsky, D.Chan, D.T.Y.Jenkinson, L.Haynes, S.Diamandakis, A.Seewooruthun, C.Addyman, A.Fiedler, S.Ryman, S.Whitehouse, J.Slater, L.H.Hadjinicolaou, A.V.Gileadi, U.Gowans, E.Shibata, Y.Barnard, M.Kaserer, T.Sharma, P.Luheshi, N.M.Wilkinson, R.W.Vaughan, T.J.Holt, S.V.Cerundolo, V.Carr, M.D.Groves, M.A.T.

(null) MAbs 12: 1801230-1801230

  • DOI: 10.1080/19420862.2020.1801230
  • Primary Citation of Related Structures:  
    6SS0, 6SS2, 6SS4, 6SRV, 6SRX, 6TUL

  • PubMed Abstract: 
  • Arginase 2 (ARG2) is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of L-arginine. The dysregulated expression of ARG2 within specific tumor microenvironments generates an immunosuppressive niche that effectively renders the tumor 'inv ...

    Arginase 2 (ARG2) is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of L-arginine. The dysregulated expression of ARG2 within specific tumor microenvironments generates an immunosuppressive niche that effectively renders the tumor 'invisible' to the host's immune system. Increased ARG2 expression leads to a concomitant depletion of local L-arginine levels, which in turn leads to suppression of anti-tumor T-cell-mediated immune responses. Here we describe the isolation and characterization of a high affinity antibody (C0021158) that inhibits ARG2 enzymatic function completely, effectively restoring T-cell proliferation in vitro . Enzyme kinetic studies confirmed that C0021158 exhibits a noncompetitive mechanism of action, inhibiting ARG2 independently of L-arginine concentrations. To elucidate C0021158's inhibitory mechanism at a structural level, the co-crystal structure of the Fab in complex with trimeric ARG2 was solved. C0021158's epitope was consequently mapped to an area some distance from the enzyme's substrate binding cleft, indicating an allosteric mechanism was being employed. Following C0021158 binding, distinct regions of ARG2 undergo major conformational changes. Notably, the backbone structure of a surface-exposed loop is completely rearranged, leading to the formation of a new short helix structure at the Fab-ARG2 interface. Moreover, this large-scale structural remodeling at ARG2's epitope translates into more subtle changes within the enzyme's active site. An arginine residue at position 39 is reoriented inwards, sterically impeding the binding of L-arginine. Arg39 is also predicted to alter the p K A of a key catalytic histidine residue at position 160, further attenuating ARG2's enzymatic function. In silico molecular docking simulations predict that L-arginine is unable to bind effectively when antibody is bound, a prediction supported by isothermal calorimetry experiments using an L-arginine mimetic. Specifically, targeting ARG2 in the tumor microenvironment through the application of C0021158, potentially in combination with standard chemotherapy regimens or alternate immunotherapies, represents a potential new strategy to target immune cold tumors.


    Organizational Affiliation

    Antibody Discovery & Protein Engineering, BioPharmaceuticals R&D, AstraZeneca , Cambridge, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginase-2, mitochondrial AAA339Homo sapiensMutation(s): 0 
Gene Names: ARG2
EC: 3.5.3.1
Find proteins for P78540 (Homo sapiens)
Explore P78540 
Go to UniProtKB:  P78540
NIH Common Fund Data Resources
PHAROS:  P78540
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab C0021158 heavy chain (IgG1) HHH233Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab C0021158 light chain (IgG1) LLL220Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AAA, HHH, LLL
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AAA, HHH, LLL
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
AAA
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AAAL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.254 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.061α = 90
b = 149.061β = 90
c = 123.287γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC1362/A20263

Revision History 

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references, Derived calculations