Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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This is version 1.5 of the entry. See complete history


Structural Basis for the Altered Activity of Gly794 Variants of Escherichia coli Beta-Galactosidase

Juers, D.H.Hakda, S.Matthews, B.W.Huber, R.E.

(2003) Biochemistry 42: 13505-13511

  • DOI: https://doi.org/10.1021/bi035506j
  • Primary Citation of Related Structures:  
    1PX3, 1PX4

  • PubMed Abstract: 

    The open-closed conformational switch in the active site of Escherichia coli beta-galactosidase was studied by X-ray crystallography and enzyme kinetics. Replacement of Gly794 by alanine causes the apoenzyme to adopt the closed rather than the open conformation. Binding of the competitive inhibitor isopropyl thio-beta-D-galactoside (IPTG) requires the mutant enzyme to adopt its less favored open conformation, weakening affinity relative to wild type. In contrast, transition-state inhibitors bind to the enzyme in the closed conformation, which is favored for the mutant, and display increased affinity relative to wild type. Changes in affinity suggest that the free energy difference between the closed and open forms is 1-2 kcal/mol. By favoring the closed conformation, the substitution moves the resting state of the enzyme along the reaction coordinate relative to the native enzyme and destabilizes the ground state relative to the first transition state. The result is that the rate constant for galactosylation is increased but degalactosylation is slower. The covalent intermediate may be better stabilized than the second transition state. The substitution also results in better binding of glucose to both the free and the galactosylated enzyme. However, transgalactosylation with glucose to produce allolactose (the inducer of the lac operon) is slower with the mutant than with the native enzyme. This suggests either that the glucose is misaligned for the reaction or that the galactosylated enzyme with glucose bound is stabilized relative to the transition state for transgalactosylation.

  • Organizational Affiliation

    Howard Hughes Medical Institute, Institute of Molecular Biology, and Department of Physics, 1229, University of Oregon, Eugene, Oregon 97403-1229, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
1,023Escherichia coliMutation(s): 1 
Gene Names: lacZ
Find proteins for P00722 (Escherichia coli (strain K12))
Explore P00722 
Go to UniProtKB:  P00722
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00722
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IPT

Download Ideal Coordinates CCD File 
GD [auth D],
M [auth A],
SA [auth B],
YB [auth C]
1-methylethyl 1-thio-beta-D-galactopyranoside
C9 H18 O5 S
Query on DMS

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AC [auth C]
AE [auth D]
BA [auth A]
AA [auth A],
AB [auth B],
AC [auth C],
AE [auth D],
BA [auth A],
BB [auth B],
BC [auth C],
BE [auth D],
CA [auth A],
CB [auth B],
CC [auth C],
CE [auth D],
DA [auth A],
DB [auth B],
DC [auth C],
DE [auth D],
EA [auth A],
EB [auth B],
EC [auth C],
FA [auth A],
FB [auth B],
FC [auth C],
GA [auth A],
GB [auth B],
GC [auth C],
HA [auth A],
HB [auth B],
HC [auth C],
HD [auth D],
IA [auth A],
IB [auth B],
IC [auth C],
ID [auth D],
JA [auth A],
JB [auth B],
JC [auth C],
JD [auth D],
KA [auth A],
KB [auth B],
KC [auth C],
KD [auth D],
LB [auth B],
LC [auth C],
LD [auth D],
MB [auth B],
MC [auth C],
MD [auth D],
N [auth A],
NB [auth B],
NC [auth C],
ND [auth D],
O [auth A],
OB [auth B],
OC [auth C],
OD [auth D],
P [auth A],
PC [auth C],
PD [auth D],
Q [auth A],
QC [auth C],
QD [auth D],
R [auth A],
RC [auth C],
RD [auth D],
S [auth A],
SC [auth C],
SD [auth D],
T [auth A],
TA [auth B],
TC [auth C],
TD [auth D],
U [auth A],
UA [auth B],
UC [auth C],
UD [auth D],
V [auth A],
VA [auth B],
VC [auth C],
VD [auth D],
W [auth A],
WA [auth B],
WC [auth C],
WD [auth D],
X [auth A],
XA [auth B],
XC [auth C],
XD [auth D],
Y [auth A],
YA [auth B],
YD [auth D],
Z [auth A],
ZA [auth B],
ZB [auth C],
ZD [auth D]
C2 H6 O S
Query on MG

Download Ideal Coordinates CCD File 
AD [auth D]
E [auth A]
F [auth A]
FD [auth D]
G [auth A]
AD [auth D],
E [auth A],
F [auth A],
FD [auth D],
G [auth A],
L [auth A],
LA [auth B],
MA [auth B],
PB [auth C],
QB [auth C],
RA [auth B],
RB [auth C],
SB [auth C],
XB [auth C],
YC [auth D],
ZC [auth D]
Query on NA

Download Ideal Coordinates CCD File 
BD [auth D]
CD [auth D]
DD [auth D]
ED [auth D]
H [auth A]
BD [auth D],
CD [auth D],
DD [auth D],
ED [auth D],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
NA [auth B],
OA [auth B],
PA [auth B],
QA [auth B],
TB [auth C],
UB [auth C],
VB [auth C],
WB [auth C]
Binding Affinity Annotations 
IDSourceBinding Affinity
IPT BindingDB:  1PX4 Ki: 7.60e+4 (nM) from 1 assay(s)
PDBBind:  1PX4 Ki: 5.90e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.49α = 90
b = 168.29β = 90
c = 200.44γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2021-10-27
    Changes: Database references, Structure summary
  • Version 1.5: 2023-08-16
    Changes: Data collection, Refinement description