3MUY

E. coli (lacZ) beta-galactosidase (R599A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Importance of Arg-599 of beta-galactosidase (Escherichia coli) as an anchor for the open conformations of Phe-601 and the active-site loop

Dugdale, M.L.Vance, M.L.Wheatley, R.W.Driedger, M.R.Nibber, A.Tran, A.Huber, R.E.

(2010) Biochem Cell Biol 88: 969-979

  • DOI: https://doi.org/10.1139/O10-144
  • Primary Citation of Related Structures:  
    3MUY

  • PubMed Abstract: 

    Structural and kinetic data show that Arg-599 of β-galactosidase plays an important role in anchoring the "open" conformations of both Phe-601 and an active-site loop (residues 794-803). When alanine was substituted for Arg-599, the conformations of Phe-601 and the loop shifted towards the "closed" positions because interactions with the guanidinium side chain were lost. Also, Phe-601, the loop, and Na+, which is ligated by the backbone carbonyl of Phe-601, lost structural order, as indicated by large B-factors. IPTG, a substrate analog, restored the conformations of Phe-601 and the loop of R599A-β-galactosidase to the open state found with IPTG-complexed native enzyme and partially reinstated order. ᴅ-Galactonolactone, a transition state analog, restored the closed conformations of R599A-β-galactosidase to those found with ᴅ-galactonolactone-complexed native enzyme and completely re-established the order. Substrates and substrate analogs bound R599A-β-galactosidase with less affinity because the closed conformation does not allow substrate binding and extra energy is required for Phe-601 and the loop to open. In contrast, transition state analog binding, which occurs best when the loop is closed, was several-fold better. The higher energy level of the enzyme•substrate complex and the lower energy level of the first transition state means that less activation energy is needed to form the first transition state and thus the rate of the first catalytic step (k2) increased substantially. The rate of the second catalytic step (k3) decreased, likely because the covalent form is more stabilized than the second transition state when Phe-601 and the loop are closed. The importance of the guanidinium group of Arg-599 was confirmed by restoration of conformation, order, and activity by guanidinium ions.


  • Organizational Affiliation

    Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-D-galactosidaseA [auth 1],
B [auth 2],
C [auth 3],
D [auth 4]
1,023Escherichia coli K-12Mutation(s): 1 
Gene Names: ECB_00298lacZ
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AB [auth 2]
AC [auth 3]
AE [auth 4]
AF [auth 4]
BB [auth 2]
AB [auth 2],
AC [auth 3],
AE [auth 4],
AF [auth 4],
BB [auth 2],
BC [auth 3],
BE [auth 4],
BF [auth 4],
CB [auth 2],
CC [auth 3],
CD [auth 3],
CE [auth 4],
CF [auth 4],
DB [auth 2],
DC [auth 3],
DD [auth 3],
DE [auth 4],
DF [auth 4],
E [auth 1],
EA [auth 1],
EB [auth 2],
EC [auth 3],
ED [auth 3],
EE [auth 4],
F [auth 1],
FA [auth 1],
FB [auth 2],
FC [auth 3],
FD [auth 3],
FE [auth 4],
G [auth 1],
GA [auth 1],
GB [auth 2],
GC [auth 3],
GD [auth 3],
GE [auth 4],
H [auth 1],
HA [auth 1],
HC [auth 3],
HD [auth 3],
HE [auth 4],
I [auth 1],
IA [auth 1],
IC [auth 3],
ID [auth 3],
IE [auth 4],
J [auth 1],
JA [auth 1],
JC [auth 3],
JD [auth 3],
JE [auth 4],
K [auth 1],
KA [auth 1],
KC [auth 3],
KD [auth 3],
KE [auth 4],
L [auth 1],
LA [auth 2],
LC [auth 3],
LD [auth 3],
LE [auth 4],
M [auth 1],
MA [auth 2],
MC [auth 3],
MD [auth 3],
ME [auth 4],
N [auth 1],
NA [auth 2],
NB [auth 2],
NC [auth 3],
ND [auth 3],
O [auth 1],
OA [auth 2],
OB [auth 2],
OC [auth 3],
OD [auth 3],
P [auth 1],
PA [auth 2],
PB [auth 2],
PC [auth 3],
PD [auth 4],
Q [auth 1],
QA [auth 2],
QB [auth 2],
QC [auth 3],
QD [auth 4],
R [auth 1],
RA [auth 2],
RB [auth 2],
RC [auth 3],
RD [auth 4],
S [auth 1],
SA [auth 2],
SB [auth 2],
SC [auth 3],
SD [auth 4],
SE [auth 4],
T [auth 1],
TA [auth 2],
TB [auth 2],
TC [auth 3],
TD [auth 4],
TE [auth 4],
U [auth 1],
UA [auth 2],
UB [auth 2],
UC [auth 3],
UD [auth 4],
V [auth 1],
VA [auth 2],
VB [auth 2],
VD [auth 4],
W [auth 1],
WA [auth 2],
WB [auth 2],
WD [auth 4],
WE [auth 4],
X [auth 1],
XA [auth 2],
XB [auth 2],
XD [auth 4],
XE [auth 4],
YA [auth 2],
YB [auth 2],
YD [auth 4],
YE [auth 4],
ZA [auth 2],
ZB [auth 3],
ZD [auth 4],
ZE [auth 4]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth 1]
HB [auth 2]
IB [auth 2]
NE [auth 4]
OE [auth 4]
AA [auth 1],
HB [auth 2],
IB [auth 2],
NE [auth 4],
OE [auth 4],
VC [auth 3],
VE [auth 4],
WC [auth 3],
Y [auth 1],
Z [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AD [auth 3]
BA [auth 1]
BD [auth 3]
CA [auth 1]
DA [auth 1]
AD [auth 3],
BA [auth 1],
BD [auth 3],
CA [auth 1],
DA [auth 1],
JB [auth 2],
KB [auth 2],
LB [auth 2],
MB [auth 2],
PE [auth 4],
QE [auth 4],
RE [auth 4],
UE [auth 4],
XC [auth 3],
YC [auth 3],
ZC [auth 3]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.266α = 90
b = 167.237β = 90
c = 200.614γ = 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: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-08-22
    Changes: Database references
  • Version 1.3: 2021-10-06
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description