PDBsum entry 3e1f

Hydrolase

PDB id

3e1f

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Contents

			Protein chains

					1011 a.a. *

			Ligands

					DMS ×73


					GAL ×8

			Metals

					_MG ×10


					_NA ×13

			Waters ×328

* Residue conservation analysis

PDB id:

3e1f

Links
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Name:

Hydrolase

Title:

E.Coli (lacz) beta-galactosidase (h418e) in complex with galactose

Structure:

Beta-galactosidase. Chain: 1, 2, 3, 4. Fragment: beta-galactosidase. Synonym: lactase. Engineered: yes. Mutation: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Gene: lacz, b0344, jw0335. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.00Å

R-factor:

0.218

R-free:

0.249

Authors:

R.E.Huber,M.L.Dugdale

Key ref:

D.H.Juers et al. (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. PubMed id: 19472413

Date:

04-Aug-08

Release date:

09-Jun-09

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

* PDB and UniProt seqs differ at 1 residue position (black cross)



		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.

	Protein Sci 18:1281-1292 (2009)
PubMed id: 19472413

Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli).
D.H.Juers, B.Rob, M.L.Dugdale, N.Rahimzadeh, C.Giang, M.Lee, B.W.Matthews, R.E.Huber.

ABSTRACT

The active site of ss-galactosidase (E. coli) contains a Mg(2+) ion ligated by Glu-416, His-418 and Glu-461 plus three water molecules. A Na(+) ion binds nearby. To better understand the role of the active site Mg(2+) and its ligands, His-418 was substituted with Asn, Glu and Phe. The Asn-418 and Glu-418 variants could be crystallized and the structures were shown to be very similar to native enzyme. The Glu-418 variant showed increased mobility of some residues in the active site, which explains why the substitutions at the Mg(2+) site also reduce Na(+) binding affinity. The Phe variant had reduced stability, bound Mg(2+) weakly and could not be crystallized. All three variants have low catalytic activity due to large decreases in the degalactosylation rate. Large decreases in substrate binding affinity were also observed but transition state analogs bound as well or better than to native. The results indicate that His-418, together with the Mg(2+), modulate the central role of Glu-461 in binding and as a general acid/base catalyst in the overall catalytic mechanism. Glucose binding as an acceptor was also dramatically decreased, indicating that His-418 is very important for the formation of allolactose (the natural inducer of the lac operon).

Literature references that cite this PDB file's key reference

PubMed id

Reference

21087993

J.Yuan, T.Gogakos, A.M.Babina, D.Söll, and L.Randau (2011).
Change of tRNA identity leads to a divergent orthogonal histidyl-tRNA synthetase/tRNAHis pair.

Nucleic Acids Res, 39, 2286-2293.

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

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

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.