PDBsum entry 1jyx

Hydrolase

PDB id

1jyx

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Contents

			Protein chains

					1011 a.a. *

			Ligands

					IPT ×6


					DMS ×74

			Metals

					_MG ×9


					_NA ×14

			Waters ×3607

* Residue conservation analysis

PDB id:

1jyx

Links

Name:

Hydrolase

Title:

E. Coli (lacz) beta-galactosidase in complex with iptg

Structure:

Beta-galactosidase. Chain: a, b, c, d. Synonym: lactase. Lacz. Beta-d-galactosidase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: lacz. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.75Å

R-factor:

0.168

R-free:

0.244

Authors:

D.H.Juers,B.W.Matthews

Key ref:

D.H.Juers et al. (2001). A structural view of the action of Escherichia coli (lacZ) beta-galactosidase. Biochemistry, 40, 14781-14794. PubMed id: 11732897 DOI: 10.1021/bi011727i

Date:

13-Sep-01

Release date:

07-Dec-01

PROCHECK

	Headers

	References

Protein chains

P00722 (BGAL_ECOLI) - Beta-galactosidase from Escherichia coli (strain K12)

Seq: Struc:

Seq: Struc:

Seq: Struc:					1024 a.a. 1011 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.2.1.23 - beta-galactosidase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.

DOI no: 10.1021/bi011727i	Biochemistry 40:14781-14794 (2001)
PubMed id: 11732897

A structural view of the action of Escherichia coli (lacZ) beta-galactosidase.
D.H.Juers, T.D.Heightman, A.Vasella, J.D.McCarter, L.Mackenzie, S.G.Withers, B.W.Matthews.

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.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21130883

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:

3og2 3ogr 3ogs 3ogv

20921997

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:

3i3b 3i3d 3i3e

21102659

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:

3muy

20544774

R.Caraballo, M.Sakulsombat, and O.Ramström (2010).
Towards dynamic drug design: identification and optimization of beta-galactosidase inhibitors from a dynamic hemithioacetal system.

Chembiochem, 11, 1600-1606.

19936901

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:

3iap 3iaq

20066263

T.M.Gloster, and G.J.Davies (2010).
Glycosidase inhibition: assessing mimicry of the transition state.

Org Biomol Chem, 8, 305-320.

19472413

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:

3dym 3dyo 3dyp 3e1f

19229596

J.C.Kappelhoff, S.Y.Liu, M.L.Dugdale, D.L.Dymianiw, L.R.Linton, and R.E.Huber (2009).
Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-beta-Galactosidase (E. coli) as Examples.

Protein J, 28, 96.

PDB code:

3czj

19966440

T.E.Klepach, M.Reed, B.C.Noll, A.G.Oliver, and A.S.Serianni (2009).
Methyl beta-allolactoside [methyl beta-D-galactopyranosyl-(1-->6)-beta-D-glucopyranoside] monohydrate.

Acta Crystallogr C, 65, o601-o606.

18227433

F.R.Salsbury, S.T.Knutson, L.B.Poole, and J.S.Fetrow (2008).
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid.

Protein Sci, 17, 299-312.

18470964

N.F.Brás, S.A.Moura-Tamames, P.A.Fernandes, and M.J.Ramos (2008).
Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates.

J Comput Chem, 29, 2565-2574.

18848471

T.M.Gloster, J.P.Turkenburg, J.R.Potts, B.Henrissat, and G.J.Davies (2008).
Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora.

Chem Biol, 15, 1058-1067.

PDB codes:

2jka 2jke 2jkp

17253128

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.

17965235

H.H.Gorris, D.M.Rissin, and D.R.Walt (2007).
Stochastic inhibitor release and binding from single-enzyme molecules.

Proc Natl Acad Sci U S A, 104, 17680-17685.

17294134

M.Sutter, S.Oliveira, N.N.Sanders, B.Lucas, A.van Hoek, M.A.Hink, A.J.Visser, S.C.De Smedt, W.E.Hennink, and W.Jiskoot (2007).
Sensitive spectroscopic detection of large and denatured protein aggregates in solution by use of the fluorescent dye Nile red.

J Fluoresc, 17, 181-192.

17661304

Y.W.Kim, H.M.Chen, J.H.Kim, J.Müllegger, D.Mahuran, and S.G.Withers (2007).
Thioglycoligase-based assembly of thiodisaccharides: screening as beta-galactosidase inhibitors.

Chembiochem, 8, 1495-1499.

16267046

E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.

J Biol Chem, 281, 1305-1308.

16193277

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.

16736094

J.A.Coker, and J.E.Brenchley (2006).
Protein engineering of a cold-active beta-galactosidase from Arthrobacter sp. SB to increase lactose hydrolysis reveals new sites affecting low temperature activity.

Extremophiles, 10, 515-524.

16356846

E.Mastrobattista, V.Taly, E.Chanudet, P.Treacy, B.T.Kelly, and A.D.Griffiths (2005).
High-throughput screening of enzyme libraries: in vitro evolution of a beta-galactosidase by fluorescence-activated sorting of double emulsions.

Chem Biol, 12, 1291-1300.

15857786

I.Matsumura, and L.A.Rowe (2005).
Whole plasmid mutagenic PCR for directed protein evolution.

Biomol Eng, 22, 73-79.

16095606

M.R.Parikh, and I.Matsumura (2005).
Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of beta-fucosidase from beta-galactosidase.

J Mol Biol, 352, 621-628.

15069062

M.L.Geddie, and I.Matsumura (2004).
Rapid evolution of beta-glucuronidase specificity by saturation mutagenesis of an active site loop.

J Biol Chem, 279, 26462-26468.

12595701

A.Varrot, and G.J.Davies (2003).
Direct experimental observation of the hydrogen-bonding network of a glycosidase along its reaction coordinate revealed by atomic resolution analyses of endoglucanase Cel5A.

Acta Crystallogr D Biol Crystallogr, 59, 447-452.

PDB codes:

1h11 1h2j 1hf6

14621996

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:

1px3 1px4

12949099

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.

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.