4TTG

Beta-galactosidase (E. coli) in the presence of potassium chloride.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Elucidating factors important for monovalent cation selectivity in enzymes: E. coli beta-galactosidase as a model.

Wheatley, R.W.Juers, D.H.Lev, B.B.Huber, R.E.Noskov, S.Y.

(2015) Phys Chem Chem Phys 17: 10899-10909

  • DOI: 10.1039/c4cp04952g
  • Primary Citation of Related Structures:  
    4TTG

  • PubMed Abstract: 
  • Many enzymes require a specific monovalent cation (M(+)), that is either Na(+) or K(+), for optimal activity. While high selectivity M(+) sites in transport proteins have been extensively studied, enzyme M(+) binding sites generally have lower selectivity and are less characterized ...

    Many enzymes require a specific monovalent cation (M(+)), that is either Na(+) or K(+), for optimal activity. While high selectivity M(+) sites in transport proteins have been extensively studied, enzyme M(+) binding sites generally have lower selectivity and are less characterized. Here we study the M(+) binding site of the model enzyme E. coli β-galactosidase, which is about 10 fold selective for Na(+) over K(+). Combining data from X-ray crystallography and computational models, we find the electrostatic environment predominates in defining the Na(+) selectivity. In this lower selectivity site rather subtle influences on the electrostatic environment become significant, including the induced polarization effects of the M(+) on the coordinating ligands and the effect of second coordination shell residues on the charge distribution of the primary ligands. This work expands the knowledge of ion selectivity in proteins to denote novel mechanisms important for the selectivity of M(+) sites in enzymes.


    Organizational Affiliation

    Division of Biochemistry, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-galactosidaseA, B, C, D1023Escherichia coliMutation(s): 0 
Gene Names: lacZ
EC: 3.2.1.23
UniProt
Find proteins for Q8VNN2 (Escherichia coli)
Explore Q8VNN2 
Go to UniProtKB:  Q8VNN2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AA [auth A] , AC [auth B] , AD [auth C] , AE [auth C] , AF [auth D] , BA [auth A] , BC [auth B] , BD [auth C] , 
AA [auth A],  AC [auth B],  AD [auth C],  AE [auth C],  AF [auth D],  BA [auth A],  BC [auth B],  BD [auth C],  BE [auth C],  BF [auth D],  CA [auth A],  CC [auth B],  CD [auth C],  CE [auth C],  CF [auth D],  DA [auth A],  DB [auth B],  DC [auth B],  DD [auth C],  DE [auth C],  DF [auth D],  EA [auth A],  EB [auth B],  EC [auth B],  ED [auth C],  EE [auth D],  EF [auth D],  FA [auth A],  FB [auth B],  FC [auth B],  FD [auth C],  FF [auth D],  GA [auth A],  GB [auth B],  GC [auth B],  GD [auth C],  GF [auth D],  HA [auth A],  HB [auth B],  HC [auth B],  HD [auth C],  HF [auth D],  IA [auth A],  IB [auth B],  IC [auth B],  ID [auth C],  IF [auth D],  JA [auth A],  JB [auth B],  JC [auth B],  JD [auth C],  JF [auth D],  KA [auth A],  KB [auth B],  KC [auth B],  KD [auth C],  KF [auth D],  LA [auth A],  LB [auth B],  LD [auth C],  MA [auth A],  MB [auth B],  MD [auth C],  ME [auth D],  N [auth A],  NA [auth A],  NB [auth B],  ND [auth C],  NE [auth D],  O [auth A],  OA [auth A],  OB [auth B],  OD [auth C],  OE [auth D],  P [auth A],  PA [auth A],  PB [auth B],  PD [auth C],  PE [auth D],  Q [auth A],  QA [auth A],  QB [auth B],  QD [auth C],  QE [auth D],  R [auth A],  RA [auth A],  RB [auth B],  RD [auth C],  RE [auth D],  S [auth A],  SA [auth A],  SB [auth B],  SD [auth C],  SE [auth D],  T [auth A],  TA [auth B],  TB [auth B],  TC [auth C],  TD [auth C],  TE [auth D],  U [auth A],  UA [auth B],  UB [auth B],  UC [auth C],  UD [auth C],  UE [auth D],  V [auth A],  VA [auth B],  VB [auth B],  VC [auth C],  VD [auth C],  VE [auth D],  W [auth A],  WB [auth B],  WC [auth C],  WD [auth C],  WE [auth D],  X [auth A],  XB [auth B],  XC [auth C],  XD [auth C],  XE [auth D],  Y [auth A],  YB [auth B],  YC [auth C],  YD [auth C],  YE [auth D],  Z [auth A],  ZB [auth B],  ZC [auth C],  ZD [auth C],  ZE [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
AB [auth B] , BB [auth B] , CB [auth B] , I [auth A] , IE [auth D] , J [auth A] , JE [auth D] , K [auth A] , 
AB [auth B],  BB [auth B],  CB [auth B],  I [auth A],  IE [auth D],  J [auth A],  JE [auth D],  K [auth A],  KE [auth D],  L [auth A],  LE [auth D],  PC [auth C],  QC [auth C],  RC [auth C],  SC [auth C],  ZA [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , FE [auth D] , G [auth A] , GE [auth D] , H [auth A] , HE [auth D] , LC [auth C] , 
E [auth A],  F [auth A],  FE [auth D],  G [auth A],  GE [auth D],  H [auth A],  HE [auth D],  LC [auth C],  MC [auth C],  NC [auth C],  OC [auth C],  WA [auth B],  XA [auth B],  YA [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B, C, DL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.29α = 90
b = 168.1β = 90
c = 200.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2014-06-20 
  • Released Date: 2015-03-25 
  • Deposition Author(s): Juers, D.H.

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy