PDBsum entry 1qut

Hydrolase

PDB id: 1qut

Contents

Protein chain

312 a.a. *

Ligands

NAG

Metals

_NA

Waters ×203

* Residue conservation analysis

PDB id:

1qut

Name:

Hydrolase

Title:

The soluble lytic transglycosylase slt35 from escherichia coli in complex with n-acetylglucosamine

Structure:

Lytic murein transglycosylase b. Chain: a. Fragment: slt35. Synonym: murein hydrolase b, 35 kd soluble lytic transglycosylase, slt35. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Cellular_location: periplasm. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.44Å R-factor: 0.191 R-free: 0.256

Authors:

E.J.Van Asselt,A.J.Dijkstra,K.H.Kalk,B.Takacs,W.Keck,B.W.Dijkstra

Key ref:

E.J.van Asselt et al. (1999). Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand. Structure, 7, 1167-1180. PubMed id: 10545329 DOI: 10.1016/S0969-2126(00)80051-9

Date:

03-Jul-99 Release date: 15-Sep-99

Protein chain

P41052  (MLTB_ECOLI) -  Membrane-bound lytic murein transglycosylase B from Escherichia coli (strain K12)

Seq: 361 a.a.

Struc: 312 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.2.2.n1 - ?????

DOI no: 10.1016/S0969-2126(00)80051-9

Structure 7:1167-1180 (1999)

PubMed id: 10545329

Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand.

E.J.van Asselt, A.J.Dijkstra, K.H.Kalk, B.Takacs, W.Keck, B.W.Dijkstra.

ABSTRACT

BACKGROUND: Lytic transglycosylases are bacterial muramidases that catalyse the cleavage of the beta- 1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan with concomitant formation of a 1,6-anhydrobond in the MurNAc residue. These muramidases play an important role in the metabolism of the bacterial cell wall and might therefore be potential targets for the rational design of antibacterial drugs. One of the lytic transglycosylases is Slt35, a naturally occurring soluble fragment of the outer membrane bound lytic transglycosylase B (MltB) from Escherichia coli. RESULTS: The crystal structure of Slt35 has been determined at 1.7 A resolution. The structure reveals an ellipsoid molecule with three domains called the alpha, beta and core domains. The core domain is sandwiched between the alpha and beta domains. Its fold resembles that of lysozyme, but it contains a single metal ion binding site in a helix-loop-helix module that is surprisingly similar to the eukaryotic EF-hand calcium-binding fold. Interestingly, the Slt35 EF-hand loop consists of 15 residues instead of the usual 12 residues. The only other prokaryotic proteins with an EF-hand motif identified so far are the D-galactose-binding proteins. Residues from the alpha and core domains form a deep groove where the substrate fragment GlcNAc can be bound. CONCLUSIONS: The three-domain structure of Slt35 is completely different from the Slt70 structure, the only other lytic transglycosylase of known structure. Nevertheless, the core domain of Slt35 closely resembles the fold of the catalytic domain of Slt70, despite the absence of any obvious sequence similarity. Residue Glu162 of Slt35 is in an equivalent position to Glu478, the catalytic acid/base of Slt70. GlcNAc binds close to Glu162 in the deep groove. Moreover, mutation of Glu162 into a glutamine residue yielded a completely inactive enzyme. These observations indicate the location of the active site and strongly support a catalytic role for Glu162.

Selected figure(s)

Figure 3.
Figure 3. The metal ion binding sites in (a) Slt35 and (b) carp parvalbumin B (PDB entry code 5cpv). (c,d) Superposition of the metal ion binding sites in Slt35 and parvalbumin B. Part (c) shows a close-up of the binding site, (d) shows the orientation and position of the EF-hand helices in the two proteins. Residues 90-98 of parvalbumin B (green) were superimposed on residues 237-245 of Slt35 (blue) with an rmsd of 0.32 Å 2 for nine Ca atoms. Residues of Slt35 that were not used in the superposition are shown in yellow. Helices E and F (green) belong to parvalbumin and the a helices H10 and H11 (yellow) are from Slt35.

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1167-1180) copyright 1999.

Figure was selected by the author.