PDBsum entry 2exb

Hydrolase

PDB id

2exb

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Contents

			Protein chain

					446 a.a. *

			Ligands

					FXM


					GOL

			Waters ×175

* Residue conservation analysis

PDB id:

2exb

Links

Name:

Hydrolase

Title:

Crystal structure of penicillin binding protein 4 (dacb) from escherichia coli, complexed with flomox

Structure:

Penicillin-binding protein 4. Chain: a. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: dh5 alpha. Gene: dacb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.75Å

R-factor:

0.211

R-free:

0.261

Authors:

H.Kishida,S.Unzai,D.I.Roper,A.Lloyd,S.-Y.Park,J.R.H.Tame

Key ref:

H.Kishida et al. (2006). Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics. Biochemistry, 45, 783-792. PubMed id: 16411754 DOI: 10.1021/bi051533t

Date:

08-Nov-05

Release date:

13-Jun-06

PROCHECK

	Headers

	References

Protein chain

P24228 (DACB_ECOLI) - D-alanyl-D-alanine carboxypeptidase DacB from Escherichia coli (strain K12)

Seq: Struc:					477 a.a. 446 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class 1:

E.C.3.4.16.4 - serine-type D-Ala-D-Ala carboxypeptidase.

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

Reaction:

D-alanyl-D-alanine + H₂O = 2 D-alanine

2 ×
Bound ligand (Het Group name = GOL)
matches with 50.00% similarity

Enzyme class 2:

E.C.3.4.21.- - ?????

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

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/bi051533t	Biochemistry 45:783-792 (2006)
PubMed id: 16411754

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics.
H.Kishida, S.Unzai, D.I.Roper, A.Lloyd, S.Y.Park, J.R.Tame.

ABSTRACT

The crystal structure of penicillin binding protein 4 (PBP4) from Escherichia coli, which has both DD-endopeptidase and DD-carboxypeptidase activity, is presented. PBP4 is one of 12 penicillin binding proteins in E. coli involved in the synthesis and maintenance of the cell wall. The model contains a penicillin binding domain similar to known structures, but includes a large insertion which folds into domains with unique folds. The structures of the protein covalently attached to five different antibiotics presented here show the active site residues are unmoved compared to the apoprotein, but nearby surface loops and helices are displaced in some cases. The altered geometry of conserved active site residues compared with those of other PBPs suggests a possible cause for the slow deacylation rate of PBP4.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20192190

P.I.O'Daniel, J.Zajicek, W.Zhang, Q.Shi, J.F.Fisher, and S.Mobashery (2010).
Elucidation of the structure of the membrane anchor of penicillin-binding protein 5 of Escherichia coli.

J Am Chem Soc, 132, 4110-4118.

18986991

A.J.Powell, J.Tomberg, A.M.Deacon, R.A.Nicholas, and C.Davies (2009).
Crystal structures of penicillin-binding protein 2 from penicillin-susceptible and -resistant strains of Neisseria gonorrhoeae reveal an unexpectedly subtle mechanism for antibiotic resistance.

J Biol Chem, 284, 1202-1212.

PDB codes:

3equ 3eqv

19672877

D.C.Marciano, N.G.Brown, and T.Palzkill (2009).
Analysis of the plasticity of location of the Arg244 positive charge within the active site of the TEM-1 beta-lactamase.

Protein Sci, 18, 2080-2089.

19413336

S.Peddi, R.A.Nicholas, and W.G.Gutheil (2009).
Neisseria gonorrhoeae penicillin-binding protein 3 demonstrates a pronounced preference for N(epsilon)-acylated substrates.

Biochemistry, 48, 5731-5737.

18602645

E.Sauvage, A.J.Powell, J.Heilemann, H.R.Josephine, P.Charlier, C.Davies, and R.F.Pratt (2008).
Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle.

J Mol Biol, 381, 383-393.

PDB codes:

2vgj 2vgk 3beb 3bec

18266856

E.Sauvage, F.Kerff, M.Terrak, J.A.Ayala, and P.Charlier (2008).
The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis.

FEMS Microbiol Rev, 32, 234-258.

18266855

W.Vollmer, B.Joris, P.Charlier, and S.Foster (2008).
Bacterial peptidoglycan (murein) hydrolases.

FEMS Microbiol Rev, 32, 259-286.

17894439

I.Kumar, H.R.Josephine, and R.F.Pratt (2007).
Reactions of peptidoglycan-mimetic beta-lactams with penicillin-binding proteins in vivo and in membranes.

ACS Chem Biol, 2, 620-624.

17888003

M.Firczuk, and M.Bochtler (2007).
Folds and activities of peptidoglycan amidases.

FEMS Microbiol Rev, 31, 676-691.

16911039

P.Macheboeuf, C.Contreras-Martel, V.Job, O.Dideberg, and A.Dessen (2006).
Penicillin binding proteins: key players in bacterial cell cycle and drug resistance processes.

FEMS Microbiol Rev, 30, 673-691.

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.