4Q24

Crystal structure of Cyclo(L-leucyl-L-phenylalanyl) synthase

PDB DOI: https://doi.org/10.2210/pdb4Q24/pdb

Classification: transferase/transferase inhibitor
Organism(s): Streptomyces noursei
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-04-07 Released: 2014-10-08
Deposition Author(s): Moutiez, M., Schmitt, E., Seguin, J., Thai, R., Favry, E., Mechulam, Y., Gondry, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.253
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases.

Moutiez, M., Schmitt, E., Seguin, J., Thai, R., Favry, E., Belin, P., Mechulam, Y., Gondry, M.

(2014) Nat Commun 5: 5141-5141

PubMed: 25284085 Search on PubMed
DOI: https://doi.org/10.1038/ncomms6141
Primary Citation of Related Structures:
4Q24

PubMed Abstract:
Cyclodipeptide synthases form cyclodipeptides from two aminoacyl transfer RNAs. They use a ping-pong mechanism that begins with transfer of the aminoacyl moiety of the first aminoacyl tRNA onto a conserved serine, yielding an aminoacyl enzyme. Combining X-ray crystallography, site-directed mutagenesis and affinity labelling of the cyclodipeptide synthase AlbC, we demonstrate that the covalent intermediate reacts with the aminoacyl moiety of the second aminoacyl tRNA, forming a dipeptidyl enzyme, and identify the aminoacyl-binding sites of the aminoacyl tRNAs.

Organizational Affiliation

Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette, France.

Macromolecule Content

Total Structure Weight: 28.23 kDa
Atom Count: 1,804
Modelled Residue Count: 224
Deposited Residue Count: 247
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclo(L-leucyl-L-phenylalanyl) synthase	A	247	Streptomyces noursei	Mutation(s): 1 Gene Names: albC EC: 2.3.2.20
UniProt
Find proteins for Q8GED7 (Streptomyces noursei) Explore Q8GED7 Go to UniProtKB: Q8GED7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8GED7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XVE Query on XVE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHENYLMETHYL N-[(2S)-4-CHLORO-3-OXO-1-PHENYL-BUTAN-2-YL]CARBAMATE C₁₈ H₁₈ Cl N O₃ OYHLRJGDELITAF-INIZCTEOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.253
R-Value Work: 0.201
R-Value Observed: 0.203
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.968	α = 90
b = 86.968	β = 90
c = 70.738	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-08
Type: Initial release
Version 1.1: 2014-12-31
Changes: Database references
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description