4H2X

Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and an analogue of glycyl adenylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Adaptation of aminoacyl-tRNA synthetase catalytic core to carrier protein aminoacylation.

Mocibob, M.Ivic, N.Luic, M.Weygand-Durasevic, I.

(2013) Structure 21: 614-626

  • DOI: 10.1016/j.str.2013.02.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amino acid:[carrier protein] ligases (aa:CP ligases) are recently discovered enzymes that are highly similar to class II aminoacyl-tRNA synthetases (aaRSs). However, while aaRSs aminoacylate tRNA and supply building blocks for ribosomal translation, ...

    Amino acid:[carrier protein] ligases (aa:CP ligases) are recently discovered enzymes that are highly similar to class II aminoacyl-tRNA synthetases (aaRSs). However, while aaRSs aminoacylate tRNA and supply building blocks for ribosomal translation, aa:CP ligases transfer activated amino acids to the phosphopantetheine group of small carrier proteins. We have solved the crystal structure of an aa:CP ligase complexed with the carrier protein (CP). The CP prosthetic group enters the active site from a different direction than tRNA in class II aaRS complexes through an idiosyncratic tunnel. CP binds to aa:CP ligase in a fundamentally different manner compared to tRNA binding by structurally closely related aaRSs. Based on crystallographic analysis, an enzyme of altered CP specificity was designed, and the mechanism of amino acid transfer to the prosthetic group was proposed. The presented study reveals how a conserved class II aaRS catalytic core can adapt to another function through minor structural alterations.


    Related Citations: 
    • Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis
      Mocibob, M.,Ivic, N.,Bilokapic, S.,Maier, T.,Luic, M.,Ban, N.,Weygand-Durasevic, I.
      () Proc.Natl.Acad.Sci.USA --: --


    Organizational Affiliation

    Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amino acid--[acyl-carrier-protein] ligase 1
A
346Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)Mutation(s): 0 
EC: 6.2.1.n2
Find proteins for Q89VT8 (Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110))
Go to UniProtKB:  Q89VT8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Amino acid--[acyl-carrier-protein] ligase 1
B
346Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)Mutation(s): 0 
EC: 6.2.1.n2
Find proteins for Q89VT8 (Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110))
Go to UniProtKB:  Q89VT8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Aminoacyl carrier protein
C, D
103Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
Find proteins for A9CHM9 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  A9CHM9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PNS
Query on PNS

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Download CCD File 
C, D
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
G5A
Query on G5A

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Download CCD File 
A, B
5'-O-(glycylsulfamoyl)adenosine
C12 H17 N7 O7 S
AMWPZASLDLLQFT-JJNLEZRASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.575α = 90.00
b = 101.433β = 90.00
c = 103.044γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
DNAdata collection
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-04-10
    Type: Database references
  • Version 1.2: 2013-05-29
    Type: Database references
  • Version 1.3: 2013-06-19
    Type: Atomic model
  • Version 1.4: 2017-08-23
    Type: Refinement description, Source and taxonomy