3I3B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, B, C, D
1,023Escherichia coli K-12Mutation(s): 1 
Gene Names: lacz
EC: 3.2.1.23
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
149
Query on 149

Download Ideal Coordinates CCD File 
E [auth A],
GC [auth C],
RA [auth B],
UD [auth D]
D-galactonolactone
C6 H10 O6
PHOQVHQSTUBQQK-MGCNEYSASA-N
DMS
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]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
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]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
149 PDBBind:  3I3B Ki: 5.90e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



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