4NEO

Structure of BlmI, a type-II acyl-carrier-protein from Streptomyces verticillus involved in bleomycin biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins.

Lohman, J.R.Ma, M.Cuff, M.E.Bigelow, L.Bearden, J.Babnigg, G.Joachimiak, A.Phillips, G.N.Shen, B.

(2014) Proteins 82: 1210-1218


  • PubMed Abstract: 
  • Carrier proteins (CPs) play a critical role in the biosynthesis of various natural products, especially in nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzymology, where the CPs are referred to as peptidyl-carrier proteins (PC ...

    Carrier proteins (CPs) play a critical role in the biosynthesis of various natural products, especially in nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzymology, where the CPs are referred to as peptidyl-carrier proteins (PCPs) or acyl-carrier proteins (ACPs), respectively. CPs can either be a domain in large multifunctional polypeptides or standalone proteins, termed Type I and Type II, respectively. There have been many biochemical studies of the Type I PKS and NRPS CPs, and of Type II ACPs. However, recently a number of Type II PCPs have been found and biochemically characterized. In order to understand the possible interaction surfaces for combinatorial biosynthetic efforts we crystallized the first characterized and representative Type II PCP member, BlmI, from the bleomycin biosynthetic pathway from Streptomyces verticillus ATCC 15003. The structure is similar to CPs in general but most closely resembles PCPs. Comparisons with previously determined PCP structures in complex with catalytic domains reveals a common interaction surface. This surface is highly variable in charge and shape, which likely confers specificity for interactions. Previous nuclear magnetic resonance (NMR) analysis of a prototypical Type I PCP excised from the multimodular context revealed three conformational states. Comparison of the states with the structure of BlmI and other PCPs reveals that only one of the NMR states is found in other studies, suggesting the other two states may not be relevant. The state represented by the BlmI crystal structure can therefore serve as a model for both Type I and Type II PCPs.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide synthetase NRPS type II-PCP
A
93Streptomyces verticillusMutation(s): 0 
Gene Names: blmI
Find proteins for Q9XC48 (Streptomyces verticillus)
Go to UniProtKB:  Q9XC48
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG0
Query on PG0

Download SDF File 
Download CCD File 
A
2-(2-METHOXYETHOXY)ETHANOL
PEG 6000
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.441α = 90.00
b = 73.441β = 90.00
c = 43.331γ = 120.00
Software Package:
Software NamePurpose
CCP4phasing
PDB_EXTRACTdata extraction
HKL-3000phasing
DENZOdata reduction
MLPHAREphasing
ARP/wARPmodel building
SCALEPACKdata scaling
HKL-3000data scaling
DMphasing
SOLVEphasing
SHELXEmodel building
Omodel building
Cootmodel building
REFMACrefinement
HKL-3000data reduction
RESOLVEphasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Structure summary
  • Version 1.2: 2014-03-19
    Type: Database references
  • Version 1.3: 2014-09-03
    Type: Database references
  • Version 1.4: 2017-11-15
    Type: Refinement description