6XJ5

Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.271 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly.

Ahmad, R.Tyryshkin, A.M.Xie, L.Hansen, W.A.Yachnin, B.J.Emge, T.J.Mashrai, A.Khare, S.D.Knapp, S.

(2023) J Inorg Biochem 244: 112206-112206

  • DOI: https://doi.org/10.1016/j.jinorgbio.2023.112206
  • Primary Citation of Related Structures:  
    6XJ5

  • PubMed Abstract: 

    Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene ("BMIE"), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu ++ and Zn ++ in bidentate (N 2 ) and tridentate (N 2 S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn ++ , Cu ++ , and Co ++ . EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu ++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H 2 O/HO - , tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn ++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. These features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.


  • Organizational Affiliation

    Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase G2
A, C, E, G
411Pseudomonas sp. RS-16Mutation(s): 1 
Gene Names: cpg2
EC: 3.4.17.11
UniProt
Find proteins for P06621 (Pseudomonas sp. (strain RS-16))
Explore P06621 
Go to UniProtKB:  P06621
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06621
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase G2
B, D, F, H
411Pseudomonas sp. RS-16Mutation(s): 1 
Gene Names: cpg2
EC: 3.4.17.11
UniProt
Find proteins for P06621 (Pseudomonas sp. (strain RS-16))
Explore P06621 
Go to UniProtKB:  P06621
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06621
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C],
X [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth F]
BA [auth D]
BB [auth G]
CA [auth D]
CB [auth G]
AB [auth F],
BA [auth D],
BB [auth G],
CA [auth D],
CB [auth G],
DA [auth D],
DB [auth G],
EA [auth D],
EB [auth H],
FA [auth D],
FB [auth H],
GA [auth D],
GB [auth H],
HA [auth D],
HB [auth H],
I [auth A],
IA [auth D],
IB [auth H],
J [auth A],
JA [auth D],
JB [auth H],
K [auth A],
KA [auth E],
KB [auth H],
L [auth A],
LA [auth E],
LB [auth H],
M [auth A],
MA [auth E],
MB [auth H],
N [auth A],
NA [auth E],
NB [auth H],
O [auth A],
OA [auth E],
P [auth B],
PA [auth E],
Q [auth B],
QA [auth E],
R [auth B],
RA [auth E],
S [auth B],
SA [auth F],
T [auth B],
TA [auth F],
U [auth C],
UA [auth F],
V [auth C],
VA [auth F],
W [auth C],
WA [auth F],
XA [auth F],
Y [auth C],
YA [auth F],
Z [auth C],
ZA [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
V44
Query on V44
B, D, F, H
L-PEPTIDE LINKINGC13 H19 N5 O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.271 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.12α = 90
b = 188.46β = 90.17
c = 124.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
PHASERphasing
xia2data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM132565

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection, Derived calculations