1JYV

E. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH ONPG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase

Juers, D.H.Heightman, T.D.Vasella, A.McCarter, J.D.Mackenzie, L.Withers, S.G.Matthews, B.W.

(2001) Biochemistry 40: 14781-14794

  • DOI: https://doi.org/10.1021/bi011727i
  • Primary Citation of Related Structures:  
    1JYN, 1JYV, 1JYW, 1JYX, 1JZ2, 1JZ3, 1JZ4, 1JZ5, 1JZ6, 1JZ7, 1JZ8, 4V44, 4V45

  • PubMed Abstract: 

    The structures of a series of complexes designed to mimic intermediates along the reaction coordinate for beta-galactosidase are presented. These complexes clarify and enhance previous proposals regarding the catalytic mechanism. The nucleophile, Glu537, is seen to covalently bind to the galactosyl moiety. Of the two potential acids, Mg(2+) and Glu461, the latter is in better position to directly assist in leaving group departure, suggesting that the metal ion acts in a secondary role. A sodium ion plays a part in substrate binding by directly ligating the galactosyl 6-hydroxyl. The proposed reaction coordinate involves the movement of the galactosyl moiety deep into the active site pocket. For those ligands that do bind deeply there is an associated conformational change in which residues within loop 794-804 move up to 10 A closer to the site of binding. In some cases this can be inhibited by the binding of additional ligands. The resulting restricted access to the intermediate helps to explain why allolactose, the natural inducer for the lac operon, is the preferred product of transglycosylation.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-Galactosidase
A, B, C, D
1,023Escherichia coliMutation(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
145
Query on 145

Download Ideal Coordinates CCD File 
HC [auth C]
IC [auth C]
N [auth A]
O [auth A]
SD [auth D]
HC [auth C],
IC [auth C],
N [auth A],
O [auth A],
SD [auth D],
TD [auth D],
YA [auth B],
ZA [auth B]
2-nitrophenyl beta-D-galactopyranoside
C12 H15 N O8
KUWPCJHYPSUOFW-YBXAARCKSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AD [auth C]
AE [auth D]
BA [auth A]
AA [auth A],
AB [auth B],
AD [auth C],
AE [auth D],
BA [auth A],
BB [auth B],
BD [auth C],
BE [auth D],
CA [auth A],
CB [auth B],
CD [auth C],
CE [auth D],
DA [auth A],
DB [auth B],
DD [auth C],
DE [auth D],
EA [auth A],
EB [auth B],
ED [auth C],
EE [auth D],
FA [auth A],
FB [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],
IA [auth A],
IB [auth B],
ID [auth C],
IE [auth D],
JA [auth A],
JB [auth B],
JC [auth C],
JD [auth C],
JE [auth D],
KA [auth A],
KB [auth B],
KC [auth C],
KE [auth D],
LA [auth A],
LB [auth B],
LC [auth C],
LE [auth D],
MA [auth A],
MB [auth B],
MC [auth C],
ME [auth D],
NA [auth A],
NB [auth B],
NC [auth C],
NE [auth D],
OA [auth A],
OB [auth B],
OC [auth C],
OE [auth D],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth C],
PE [auth D],
Q [auth A],
QB [auth B],
QC [auth C],
QE [auth D],
R [auth A],
RB [auth B],
RC [auth C],
RE [auth D],
S [auth A],
SB [auth B],
SC [auth C],
SE [auth D],
T [auth A],
TB [auth B],
TC [auth C],
TE [auth D],
U [auth A],
UB [auth B],
UC [auth C],
UD [auth D],
UE [auth D],
V [auth A],
VB [auth B],
VC [auth C],
VD [auth D],
VE [auth D],
W [auth A],
WB [auth B],
WC [auth C],
WD [auth D],
X [auth A],
XB [auth B],
XC [auth C],
XD [auth D],
Y [auth A],
YB [auth B],
YC [auth C],
YD [auth D],
Z [auth A],
ZC [auth C],
ZD [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth C]
BC [auth C]
CC [auth C]
E [auth A]
F [auth A]
AC [auth C],
BC [auth C],
CC [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
KD [auth D],
LD [auth D],
MD [auth D],
ND [auth D],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
ZB [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
DC [auth C]
EC [auth C]
FC [auth C]
GC [auth C]
J [auth A]
DC [auth C],
EC [auth C],
FC [auth C],
GC [auth C],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
OD [auth D],
PD [auth D],
QD [auth D],
RD [auth D],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.492α = 90
b = 167.455β = 90
c = 200.341γ = 90
Software Package:
Software NamePurpose
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-10-27
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-16
    Changes: Data collection, Refinement description