3I3E

E. COLI (lacZ) BETA-GALACTOSIDASE (M542A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-galactosidaseA, B, C, D1,023Escherichia coli K-12Mutation(s): 1 
Gene Names: lacZb0344JW0335
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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],
BF [auth D],
CA [auth A],
CB [auth B],
CC [auth B],
CD [auth C],
CF [auth D],
DA [auth A],
DB [auth B],
DC [auth B],
DD [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],
FE [auth D],
FF [auth D],
GA [auth A],
GB [auth B],
GC [auth B],
GD [auth C],
GE [auth D],
GF [auth D],
HA [auth A],
HB [auth B],
HC [auth B],
HD [auth C],
HE [auth D],
HF [auth D],
IA [auth A],
IB [auth B],
IC [auth C],
ID [auth C],
IE [auth D],
IF [auth D],
JA [auth A],
JB [auth B],
JD [auth C],
JE [auth D],
JF [auth D],
KA [auth A],
KB [auth B],
KD [auth C],
KE [auth D],
KF [auth D],
LA [auth A],
LB [auth B],
LD [auth C],
LE [auth D],
LF [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],
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],
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],
UD [auth C],
UE [auth D],
V [auth A],
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],
XE [auth D],
Y [auth A],
YB [auth B],
YC [auth C],
YE [auth D],
Z [auth A],
ZB [auth B],
ZC [auth C],
ZE [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
JC [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
JC [auth C],
KC [auth C],
LC [auth C],
MC [auth C],
SA [auth A],
TA [auth B],
UA [auth B],
VA [auth B],
XD [auth D],
YD [auth D],
ZD [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AE [auth D],
BE [auth D],
CE [auth D],
DE [auth D],
I [auth A],
AE [auth D],
BE [auth D],
CE [auth D],
DE [auth D],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
NC [auth C],
OC [auth C],
PC [auth C],
QC [auth C],
WA [auth B],
XA [auth B],
YA [auth B],
ZA [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.701α = 90
b = 168.417β = 90
c = 200.709γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



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: 2021-10-13
    Changes: Database references, Derived calculations