 |
PDBsum entry 1dp0
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Hydrolase
|
|
|
Title:
|
|
E. Coli beta-galactosidase at 1.7 angstrom
|
|
Structure:
|
|
Beta-galactosidase. Chain: a, b, c, d. Engineered: yes
|
|
Source:
|
|
Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
|
|
Biol. unit:
|
|
Tetramer (from
)
|
|
Resolution:
|
|
|
1.70Å
|
R-factor:
|
0.158
|
R-free:
|
0.211
|
|
|
Authors:
|
|
D.H.Juers,R.H.Jacobson,D.Wigley,X.J.Zhang,R.E.Huber,D.E.Tronrud, B.W.Matthews
|
|
Key ref:
|
|
D.H.Juers
et al.
(2000).
High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation.
Protein Sci,
9,
1685-1699.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
22-Dec-99
|
Release date:
|
21-Feb-01
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P00722
(BGAL_ECOLI) -
Beta-galactosidase from Escherichia coli (strain K12)
|
|
|
|
Seq:
Struc:
|
|
|
|
1024 a.a.
1011 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.3.2.1.23
- beta-galactosidase.
|
|
|
|
|
|
|
Reaction:
|
|
Hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Protein Sci
9:1685-1699
(2000)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation.
|
|
D.H.Juers,
R.H.Jacobson,
D.Wigley,
X.J.Zhang,
R.E.Huber,
D.E.Tronrud,
B.W.Matthews.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The unrefined fold of Escherichia coli beta-galactosidase based on a monoclinic
crystal form with four independent tetramers has been reported previously. Here,
we describe a new, orthorhombic form with one tetramer per asymmetric unit that
has permitted refinement of the structure at 1.7 A resolution. This
high-resolution analysis has confirmed the original description of the structure
and revealed new details. An essential magnesium ion, identified at the active
site in the monoclinic crystals, is also seen in the orthorhombic form.
Additional putative magnesium binding sites are also seen. Sodium ions are also
known to affect catalysis, and five putative binding sites have been identified,
one close to the active site. In a crevice on the protein surface, five linked
five-membered solvent rings form a partial clathrate-like structure. Some other
unusual aspects of the structure include seven apparent cis-peptide bonds, four
of which are proline, and several internal salt-bridge networks. Deep
solvent-filled channels and tunnels extend across the surface of the molecule
and pass through the center of the tetramer. Because of these departures from a
compact globular shape, the molecule is not well characterized by prior
empirical relationships between the mass and surface area of proteins. The 50 or
so residues at the amino terminus have a largely extended conformation and
mostly lie across the surface of the protein. At the same time, however, segment
13-21 contributes to a subunit interface, and residues 29-33 pass through a
"tunnel" formed by a domain interface. Taken together, the overall arrangement
provides a structural basis for the phenomenon of alpha-complementation.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
M.Maksimainen,
N.Hakulinen,
J.M.Kallio,
T.Timoharju,
O.Turunen,
and
J.Rouvinen
(2011).
Crystal structures of Trichoderma reesei β-galactosidase reveal conformational changes in the active site.
|
| |
J Struct Biol,
174,
156-163.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.Yoshida,
M.Hidaka,
S.Fushinobu,
T.Koyanagi,
H.Minami,
H.Tamaki,
M.Kitaoka,
T.Katayama,
and
H.Kumagai
(2010).
Role of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 β-glucosidase from Kluyveromyces marxianus.
|
| |
Biochem J,
431,
39-49.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Krahulec,
T.Szemes,
and
J.Krahulcová
(2010).
Bioinformatics characterization of potential new beta-glucuronidase from Streptococcus equi subsp. zooepidemicus.
|
| |
Mol Biotechnol,
44,
232-241.
|
|
|
|
|
|
|
M.L.Dugdale,
D.L.Dymianiw,
B.K.Minhas,
I.D'Angelo,
and
R.E.Huber
(2010).
Role of Met-542 as a guide for the conformational changes of Phe-601 that occur during the reaction of β-galactosidase (Escherichia coli).
|
| |
Biochem Cell Biol,
88,
861-869.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.L.Dugdale,
M.L.Vance,
R.W.Wheatley,
M.R.Driedger,
A.Nibber,
A.Tran,
and
R.E.Huber
(2010).
Importance of Arg-599 of β-galactosidase (Escherichia coli) as an anchor for the open conformations of Phe-601 and the active-site loop.
|
| |
Biochem Cell Biol,
88,
969-979.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Lo,
M.L.Dugdale,
N.Jeerh,
T.Ku,
N.J.Roth,
and
R.E.Huber
(2010).
Studies of Glu-416 variants of beta-galactosidase (E. coli) show that the active site Mg(2+) is not important for structure and indicate that the main role of Mg (2+) is to mediate optimization of active site chemistry.
|
| |
Protein J,
29,
26-31.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.H.Juers,
B.Rob,
M.L.Dugdale,
N.Rahimzadeh,
C.Giang,
M.Lee,
B.W.Matthews,
and
R.E.Huber
(2009).
Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli).
|
| |
Protein Sci,
18,
1281-1292.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.R.Nichols,
E.Shadabi,
and
D.B.Craig
(2009).
Effect of alteration of translation error rate on enzyme microheterogeneity as assessed by variation in single molecule electrophoretic mobility and catalytic activity.
|
| |
Biochem Cell Biol,
87,
517-529.
|
|
|
|
|
|
|
L.Martin,
A.Che,
and
D.Endy
(2009).
Gemini, a bifunctional enzymatic and fluorescent reporter of gene expression.
|
| |
PLoS One,
4,
e7569.
|
|
|
|
|
|
|
D.H.Juers,
J.Lovelace,
H.D.Bellamy,
E.H.Snell,
B.W.Matthews,
and
G.E.Borgstahl
(2007).
Changes to crystals of Escherichia coli beta-galactosidase during room-temperature/low-temperature cycling and their relation to cryo-annealing.
|
| |
Acta Crystallogr D Biol Crystallogr,
63,
1139-1153.
|
|
|
|
|
|
|
E.R.Nichols,
J.M.Gavina,
R.G.McLeod,
and
D.B.Craig
(2007).
Single molecule assays of beta-galactosidase from two wild-type strains of E. coli: effects of protease inhibitors on microheterogeneity and different relative activities with differing substrates.
|
| |
Protein J,
26,
95.
|
|
|
|
|
|
|
K.R.Olson,
and
R.M.Eglen
(2007).
Beta galactosidase complementation: a cell-based luminescent assay platform for drug discovery.
|
| |
Assay Drug Dev Technol,
5,
137-144.
|
|
|
|
|
|
|
H.P.Sørensen,
T.K.Porsgaard,
R.A.Kahn,
P.Stougaard,
K.K.Mortensen,
and
M.G.Johnsen
(2006).
Secreted beta-galactosidase from a Flavobacterium sp. isolated from a low-temperature environment.
|
| |
Appl Microbiol Biotechnol,
70,
548-557.
|
|
|
|
|
|
|
A.Griffiths,
and
D.M.Coen
(2005).
An unusual internal ribosome entry site in the herpes simplex virus thymidine kinase gene.
|
| |
Proc Natl Acad Sci U S A,
102,
9667-9672.
|
|
|
|
|
|
|
T.S.Wehrman,
C.L.Casipit,
N.M.Gewertz,
and
H.M.Blau
(2005).
Enzymatic detection of protein translocation.
|
| |
Nat Methods,
2,
521-527.
|
|
|
|
|
|
|
A.Hoyoux,
V.Blaise,
T.Collins,
S.D'Amico,
E.Gratia,
A.L.Huston,
J.C.Marx,
G.Sonan,
Y.Zeng,
G.Feller,
and
C.Gerday
(2004).
Extreme catalysts from low-temperature environments.
|
| |
J Biosci Bioeng,
98,
317-330.
|
|
|
|
|
|
|
A.R.Buskirk,
Y.C.Ong,
Z.J.Gartner,
and
D.R.Liu
(2004).
Directed evolution of ligand dependence: small-molecule-activated protein splicing.
|
| |
Proc Natl Acad Sci U S A,
101,
10505-10510.
|
|
|
|
|
|
|
D.H.Juers,
and
B.W.Matthews
(2004).
The role of solvent transport in cryo-annealing of macromolecular crystals.
|
| |
Acta Crystallogr D Biol Crystallogr,
60,
412-421.
|
|
|
|
|
|
|
E.Poussu,
M.Vihinen,
L.Paulin,
and
H.Savilahti
(2004).
Probing the alpha-complementing domain of E. coli beta-galactosidase with use of an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition.
|
| |
Proteins,
54,
681-692.
|
|
|
|
|
|
|
J.Xu,
M.A.McRae,
S.Harron,
B.Rob,
and
R.E.Huber
(2004).
A study of the relationships of interactions between Asp-201, Na+ or K+, and galactosyl C6 hydroxyl and their effects on binding and reactivity of beta-galactosidase.
|
| |
Biochem Cell Biol,
82,
275-284.
|
|
|
|
|
|
|
M.Hidaka,
Y.Honda,
M.Kitaoka,
S.Nirasawa,
K.Hayashi,
T.Wakagi,
H.Shoun,
and
S.Fushinobu
(2004).
Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold.
|
| |
Structure,
12,
937-947.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.Philibert,
and
P.Martineau
(2004).
Directed evolution of single-chain Fv for cytoplasmic expression using the beta-galactosidase complementation assay results in proteins highly susceptible to protease degradation and aggregation.
|
| |
Microb Cell Fact,
3,
16.
|
|
|
|
|
|
|
R.E.Campbell
(2004).
Realization of beta-lactamase as a versatile fluorogenic reporter.
|
| |
Trends Biotechnol,
22,
208-211.
|
|
|
|
|
|
|
D.H.Juers,
S.Hakda,
B.W.Matthews,
and
R.E.Huber
(2003).
Structural basis for the altered activity of Gly794 variants of Escherichia coli beta-galactosidase.
|
| |
Biochemistry,
42,
13505-13511.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.A.Coker,
P.P.Sheridan,
J.Loveland-Curtze,
K.R.Gutshall,
A.J.Auman,
and
J.E.Brenchley
(2003).
Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic arthrobacter isolate.
|
| |
J Bacteriol,
185,
5473-5482.
|
|
|
|
|
|
|
F.Mongelard,
M.Labrador,
E.M.Baxter,
T.I.Gerasimova,
and
V.G.Corces
(2002).
Trans-splicing as a novel mechanism to explain interallelic complementation in Drosophila.
|
| |
Genetics,
160,
1481-1487.
|
|
|
|
|
|
|
M.Inohara-Ochiai,
S.Hasegawa,
S.Iguchi,
T.Ashikari,
Y.Shibano,
H.Hemmi,
T.Nakayama,
and
T.Nishino
(2002).
Deletion and insertion of a 192-residue peptide in the active-site domain of glycosyl hydrolase family-2 beta-galactosidases.
|
| |
J Biosci Bioeng,
93,
575-583.
|
|
|
|
|
|
|
N.Lopes Ferreira,
and
J.H.Alix
(2002).
The DnaK chaperone is necessary for alpha-complementation of beta-galactosidase in Escherichia coli.
|
| |
J Bacteriol,
184,
7047-7054.
|
|
|
|
|
|
|
R.E.Huber,
I.Y.Hlede,
N.J.Roth,
K.C.McKenzie,
and
K.K.Ghumman
(2001).
His-391 of beta-galactosidase (Escherichia coli) promotes catalyses by strong interactions with the transition state.
|
| |
Biochem Cell Biol,
79,
183-193.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
|
Links
