E.coli (lacz) Beta-Galactosidase (M542A) in Complex with D-Galactopyranosyl-1-on

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 

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Role of Met-542 as a guide for the conformational changes of Phe-601 that occur during the reaction of β-galactosidase (Escherichia coli).

Dugdale, M.L.Dymianiw, D.L.Minhas, B.K.D'Angelo, I.Huber, R.E.

(2010) Biochem Cell Biol 88: 861-869

  • DOI: https://doi.org/10.1139/O10-009
  • Primary Citation of Related Structures:  
    3I3B, 3I3D, 3I3E

  • PubMed Abstract: 

    The Met-542 residue of β-galactosidase is important for the enzyme's activity because it acts as a guide for the movement of the benzyl side chain of Phe-601 between two stable positions. This movement occurs in concert with an important conformational change (open vs. closed) of an active site loop (residues 794-803). Phe-601 and Arg-599, which interact with each other via the π electrons of Phe-601 and the guanidium cation of Arg-599, move out of their normal positions and become disordered when Met-542 is replaced by an Ala residue because of the loss of the guide. Since the backbone carbonyl of Phe-601 is a ligand for Na(+), the Na(+) also moves out of its normal position and becomes disordered; the Na(+) binds about 120 times more poorly. In turn, two other Na(+) ligands, Asn-604 and Asp-201, become disordered. A substrate analog (IPTG) restored Arg-599, Phe-601, and Na(+) to their normal open-loop positions, whereas a transition state analog d-galactonolactone) restored them to their normal closed-loop positions. These compounds also restored order to Phe-601, Asn-604, Asp-201, and Na(+). Binding energy was, however, necessary to restore structure and order. The K(s) values of oNPG and pNPG and the competitive K(i) values of substrate analogs were 90-250 times higher than with native enzyme, whereas the competitive K(i) values of transition state analogs were ~3.5-10 times higher. Because of this, the E•S energy level is raised more than the E•transition state energy level and less activation energy is needed for galactosylation. The galactosylation rates (k₂) of M542A-β-galactosidase therefore increase. However, the rate of degalactosylation (k₃) decreased because the E•transition state complex is less stable.

  • Organizational Affiliation

    Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
1,023Escherichia coli K-12Mutation(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 149

Download Ideal Coordinates CCD File 
E [auth A],
GC [auth C],
RA [auth B],
UD [auth D]
C6 H10 O6
Query on DMS

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AC [auth B]
AD [auth C]
AF [auth D]
AA [auth A],
AB [auth B],
AC [auth B],
AD [auth C],
AF [auth D],
BA [auth A],
BB [auth B],
BC [auth B],
BD [auth C],
BE [auth D],
BF [auth D],
CA [auth A],
CB [auth B],
CC [auth B],
CD [auth C],
CE [auth D],
CF [auth D],
DA [auth A],
DB [auth B],
DC [auth B],
DD [auth C],
DE [auth D],
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],
FE [auth D],
GA [auth A],
GB [auth B],
GD [auth C],
GE [auth D],
HA [auth A],
HB [auth B],
HD [auth C],
HE [auth D],
IB [auth B],
ID [auth C],
IE [auth D],
JA [auth A],
JB [auth B],
JD [auth C],
JE [auth D],
KA [auth A],
KB [auth B],
KD [auth C],
KE [auth D],
LA [auth A],
LB [auth B],
LD [auth C],
LE [auth D],
M [auth A],
MA [auth A],
MB [auth B],
MD [auth C],
ME [auth D],
N [auth A],
NA [auth A],
NB [auth B],
NC [auth C],
ND [auth C],
NE [auth D],
O [auth A],
OA [auth A],
OB [auth B],
OC [auth C],
OD [auth C],
OE [auth D],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth C],
PD [auth C],
PE [auth D],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth C],
QD [auth C],
QE [auth D],
R [auth A],
RB [auth B],
RC [auth C],
RD [auth C],
RE [auth D],
S [auth A],
SB [auth B],
SC [auth C],
SD [auth C],
SE [auth D],
T [auth A],
TB [auth B],
TC [auth C],
TD [auth C],
TE [auth D],
U [auth A],
UB [auth B],
UC [auth C],
UE [auth D],
V [auth A],
VB [auth B],
VC [auth C],
VE [auth D],
W [auth A],
WB [auth B],
WC [auth C],
WE [auth D],
X [auth A],
XB [auth B],
XC [auth C],
XE [auth D],
Y [auth A],
YB [auth B],
YC [auth C],
YE [auth D],
Z [auth A],
ZA [auth B],
ZB [auth B],
ZC [auth C],
ZE [auth D]
C2 H6 O S
Query on MG

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F [auth A]
G [auth A]
H [auth A]
HC [auth C]
IA [auth A]
F [auth A],
G [auth A],
H [auth A],
HC [auth C],
IA [auth A],
IC [auth C],
SA [auth B],
TA [auth B],
UA [auth B],
VD [auth D],
WD [auth D]
Query on NA

Download Ideal Coordinates CCD File 
AE [auth D]
I [auth A]
J [auth A]
JC [auth C]
K [auth A]
AE [auth D],
I [auth A],
J [auth A],
JC [auth C],
K [auth A],
KC [auth C],
L [auth A],
LC [auth C],
MC [auth C],
VA [auth B],
WA [auth B],
XA [auth B],
XD [auth D],
YA [auth B],
YD [auth D],
ZD [auth D]
Binding Affinity Annotations 
IDSourceBinding Affinity
149 PDBBind:  3I3B Ki: 5.90e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.6α = 90
b = 168.42β = 90
c = 201.31γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata 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: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations
  • Version 1.4: 2021-10-13
    Changes: Database references
  • Version 1.5: 2023-09-06
    Changes: Data collection, Refinement description