8IF7 | pdb_00008if7

Crystal structure of CmnB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.225 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: in silico
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Literature

Crystal structure of CmnB involved in the biosynthesis of the nonproteinogenic amino acid L-2,3-diaminopropionic acid.

Toh, S.I.Lo, C.L.Chang, C.Y.

(2023) Acta Crystallogr F Struct Biol Commun 79: 193-199

  • DOI: https://doi.org/10.1107/S2053230X23005769
  • Primary Citation Related Structures: 
    8IF7

  • PubMed Abstract: 

    L-2,3-Diaminopropionic acid (L-Dap) is a nonproteinogenic amino acid that plays as an important role as a building block in the biosynthesis of several natural products, including capreomycin, viomycin, zwittermicin, staphyloferrin and dapdiamide. A previous study reported that CmnB and CmnK are two enzymes that are involved in the formation of L-Dap in the biosynthesis of capreomycin. CmnB catalyzes the condensation reaction of O-phospho-L-serine and L-glutamic acid to generate N-(1-amino-1-carboxyl-2-ethyl)glutamic acid, which subsequently undergoes oxidative hydrolysis via CmnK to generate the product L-Dap. Here, the crystal structure of CmnB in complex with the reaction intermediate PLP-α-aminoacrylate is reported at 2.2 Å resolution. Notably, CmnB is the second known example of a PLP-dependent enzyme that forms a monomeric structure in crystal packing. The crystal structure of CmnB also provides insights into the catalytic mechanism of the enzyme and supports the biosynthetic pathway of L-Dap reported in previous studies.


  • Organizational Affiliation
    • Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 40.77 kDa 
  • Atom Count: 2,619 
  • Modeled Residue Count: 342 
  • Deposited Residue Count: 383 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CmnB383Saccharothrix mutabilis subsp. capreolusMutation(s): 0 
Gene Names: cmnB
UniProt
Find proteins for A6YEH3 (Saccharothrix mutabilis subsp. capreolus)
Explore A6YEH3 
Go to UniProtKB:  A6YEH3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6YEH3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P1T
(Subject of Investigation/LOI)

Query on P1T



Download:Ideal Coordinates CCD File
B [auth A]2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID
C11 H15 N2 O7 P
BXUDKFHCAMQSRX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.225 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.649α = 90
b = 64.649β = 90
c = 84.189γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan110-2113-M-A49-026-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary