7TL7 | pdb_00007tl7

1.90A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Sa-D2)

PDB DOI: https://doi.org/10.2210/pdb7TL7/pdb

Classification: ISOMERASE/Inhibitor
Organism(s): Caenorhabditis elegans, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-18 Released: 2022-08-10
Deposition Author(s): Liu, L., Lovell, S., Battaile, K.P., Dranchak, P., Queme, B., Aitha, M., van Neer, R.H.P., Kimura, H., Katho, T., Suga, H., Inglese, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.216 (Depositor), 0.221 (DCC)
R-Value Work:
0.171 (Depositor), 0.178 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases.

van Neer, R.H.P., Dranchak, P.K., Liu, L., Aitha, M., Queme, B., Kimura, H., Katoh, T., Battaile, K.P., Lovell, S., Inglese, J., Suga, H.

(2022) ACS Chem Biol 17: 2284-2295

PubMed: 35904259 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acschembio.2c00403
Primary Citation Related Structures:
7TL7, 7TL8

PubMed Abstract:
N -Methylated amino acids ( N -MeAAs) are privileged residues of naturally occurring peptides critical to bioactivity. However, de novo discovery from ribosome display is limited by poor incorporation of N -methylated amino acids into the nascent peptide chain attributed to a poor EF-Tu affinity for the N -methyl-aminoacyl-tRNA. By reconfiguring the tRNA's T-stem region to compensate and tune the EF-Tu affinity, we conducted Random nonstandard Peptides Integrated Discovery (RaPID) display of a macrocyclic peptide (MCP) library containing six different N -MeAAs. We have here devised a "pool-and-split" enrichment strategy using the RaPID display and identified N -methylated MCPs against three species of prokaryotic metal-ion-dependent phosphoglycerate mutases. The enriched MCPs reached 57% N -methylation with up to three consecutively incorporated N -MeAAs, rivaling natural products. Potent nanomolar inhibitors ranging in ortholog selectivity, strongly mediated by N -methylation, were identified. Co-crystal structures reveal an architecturally related Ce-2 Ipglycermide active-site metal-ion-coordinating Cys lariat MCP, functionally dependent on two cis N -MeAAs with broadened iPGM species selectivity over the original nematode-selective MCPs. Furthermore, the isolation of a novel metal-ion-independent Staphylococcus aureus iPGM inhibitor utilizing a phosphoglycerate mimetic mechanism illustrates the diversity of possible chemotypes encoded by the N -MeAA MCP library.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.

Macromolecule Content

Total Structure Weight: 243.02 kDa
Atom Count: 17,471
Modeled Residue Count: 2,160
Deposited Residue Count: 2,196
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-bisphosphoglycerate-independent phosphoglycerate mutase	A, B, C, D	534	Caenorhabditis elegans	Mutation(s): 0 Gene Names: ipgm-1, F57B10.3 EC: 5.4.2.12
UniProt
Find proteins for G5EFZ1 (Caenorhabditis elegans) Explore G5EFZ1 Go to UniProtKB: G5EFZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G5EFZ1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide Sa-D2	E [auth a], F [auth b], G [auth c], H [auth d]	15	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C]	O [auth C], S [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain O [auth C] Focus chain S [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] L [auth B] M [auth B] P [auth C] I [auth A], J [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], T [auth D], U [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A]	K [auth A], N [auth B], R [auth C], V [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DTY Query on DTY	E [auth a], F [auth b], G [auth c], H [auth d]	D-PEPTIDE LINKING	C₉ H₁₁ N O₃		--
YNM Query on YNM	E [auth a], F [auth b], G [auth c], H [auth d]	L-PEPTIDE LINKING	C₁₀ H₁₃ N O₃		TYR

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002491 Query on PRD_002491	E [auth a], F [auth b], G [auth c], H [auth d]	Sa-D2	Cyclic peptide / Inhibitor		Interactions Focus chain E [auth a] Focus chain F [auth b] Focus chain G [auth c] Focus chain H [auth d] Interactions & Density Focus chain E [auth a] Focus chain F [auth b] Focus chain G [auth c] Focus chain H [auth d]