5YPP

Crystal structure of IlvN.Val-1a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic Structures of IlvN·Val/Ile Complexes: Conformational Selectivity for Feedback Inhibition of Aceto Hydroxy Acid Synthases.

Bansal, A.Karanth, N.M.Demeler, B.Schindelin, H.Sarma, S.P.

(2019) Biochemistry 58: 1992-2008

  • DOI: 10.1021/acs.biochem.9b00050
  • Primary Citation of Related Structures:  
    5YPP, 5YPW, 5YPY, 5YUM

  • PubMed Abstract: 
  • Conformational factors that predicate selectivity for valine or isoleucine binding to IlvN leading to the regulation of aceto hydroxy acid synthase I (AHAS I) of Escherichia coli have been determined for the first time from high-resolution (1.9-2.43 Å) crystal structures of IlvN·Val and IlvN·Ile complexes ...

    Conformational factors that predicate selectivity for valine or isoleucine binding to IlvN leading to the regulation of aceto hydroxy acid synthase I (AHAS I) of Escherichia coli have been determined for the first time from high-resolution (1.9-2.43 Å) crystal structures of IlvN·Val and IlvN·Ile complexes. The valine and isoleucine ligand binding pockets are located at the dimer interface. In the IlvN·Ile complex, among residues in the binding pocket, the side chain of Cys 43 is 2-fold disordered (χ 1 angles of gauche - and trans). Only one conformation can be observed for the identical residue in the IlvN·Val complexes. In a reversal, the side chain of His 53 , located at the surface of the protein, exhibits two conformations in the IlvN·Val complex. The concerted conformational switch in the side chains of Cys 43 and His 53 may play an important role in the regulation of the AHAS I holoenzyme activity. A significant result is the establishment of the subunit composition in the AHAS I holoenzyme by analytical ultracentrifugation. Solution nuclear magnetic resonance and analytical ultracentrifugation experiments have also provided important insights into the hydrodynamic properties of IlvN in the ligand-free and -bound states. The structural and biophysical data unequivocally establish the molecular basis for differential binding of the ligands to IlvN and a rationale for the resistance of IlvM to feedback inhibition by the branched-chain amino acids.


    Related Citations: 
    • The coil-to-helix transition in IlvN regulates the allosteric control of Escherichia coli acetohydroxyacid synthase I.
      Karanth, N.M., Sarma, S.P.
      (2013) Biochemistry 52: 70
    • Escherichia coli ilvN interacts with the FAD binding domain of ilvB and activates the AHAS I enzyme.
      Mitra, A., Sarma, S.P.
      (2008) Biochemistry 47: 1518

    Organizational Affiliation

    NMR Research Center , Indian Institute of Science , Bangalore , Karnataka 560012 , India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetolactate synthase isozyme 1 small subunitA, B, C, D, E, F98Escherichia coli K-12Mutation(s): 0 
Gene Names: ilvNb3670JW3645
EC: 2.2.1.6
UniProt
Find proteins for P0ADF8 (Escherichia coli (strain K12))
Explore P0ADF8 
Go to UniProtKB:  P0ADF8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VAL
Query on VAL

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], L [auth C], M [auth C], Q [auth E], S [auth F]VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A] , J [auth B] , K [auth B] , N [auth C] , O [auth C] , P [auth D] , R [auth E] , U [auth F] , 
I [auth A], J [auth B], K [auth B], N [auth C], O [auth C], P [auth D], R [auth E], U [auth F], V [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
T [auth F]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.03α = 90
b = 80.62β = 119.99
c = 66.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
IndiaDSTO1544

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.3: 2019-05-01
    Changes: Data collection, Database references