DD-transpeptidase

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Serine-type D-Ala-D-Ala carbboxypeptidase

Structure of the streptomyces K15 DD-transpeptidase

Identifiers

EC number 3.4.16.4

CAS number 9077-67-2

Databases

IntEnz IntEnz view

BRENDA BRENDA entry

ExPASy NiceZyme view

KEGG KEGG entry

MetaCyc metabolic pathway

PRIAM profile

PDB structures RCSB PDB PDBe PDBsum

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DD-transpeptidase (EC 3.4.16.4, DD-peptidase, DD-transpeptidase, DD-carboxypeptidase, D-

alanyl-D-alanine carboxypeptidase, D-alanyl-D-alanine-cleaving-peptidase, D-alanine
carboxypeptidase, D-alanyl carboxypeptidase, and serine-type D-Ala-D-Ala carboxypeptidase.[1])
 is a bacterial enzyme that catalyzes the transfer of the R-Laca-D-alanyl moiety of R-L-aca-D-
alanyl-D-alanine carbonyl donors to the -OH of their active-site serine and from this to a final
acceptor.[2] It is involved in bacterial cell wall biosynthesis, namely, the transpeptidation that
crosslinks the peptide side chains of peptidoglycan strands.[3]
The antibiotic penicillin irreversibly binds to and inhibits the activity of the transpeptidase enzyme
by forming a highly stable penicilloyl-enzyme intermediate.[4] Because of the interaction between
penicillin and transpeptidase, this enzyme is also known as penicillin-binding protein (PBP).

Contents
[hide]

1Mechanism

2Structure

3Biological Function

4Disease Relevance

5See also

6References

7External links

Mechanism[edit]
DD-transpeptidase is mechanistically similar to the proteolytic reactions of the trypsin protein
family.[5]
DD-transpeptidase catalytic mechanism
Crosslinking of peptidyl moieties of adjacent glycan strands is a two-step reaction. The first step
involves the cleavage of the D-alanyl-D-alanine bond of a peptide unit precursor acting as
carbonyl donor, the release of the carboxyl-terminal D-alanine, and the formation of the acyl-
enzyme. The second step involves the breakdown of the acyl-enzyme intermediate and the
formation of a new peptide bond between the carbonyl of the D-alanyl moiety and theamino
group of another peptide unit.[6]
Most discussion of DD-peptidase mechanisms revolves around the catalysts of proton transfer.
During formation of the acyl-enzyme intermediate, a proton must be removed from the active site
serine hydroxyl group and one must be added to the amine leaving group. A similar proton
movement must be facilitated in deacylation. The identity of the general acid and base catalysts
involved in these proton transfers has not yet been elucidated. [7] However, the catalytic triad
tyrosine, lysine, and serine, as well as serine, lysine, serine have been proposed. [7]

Structure[edit]
Transpeptidases are members of the penicilloyl-serine transferase superfamily, which has a
signature SxxK conserved motif.[8] With "x" denoting a variable amino acid residue, the
transpeptidases of this superfamily show a trend in the form of three motifs: SxxK, SxN (or
analogue), and KTG (or analogue). These motifs occur at equivalent places, and are roughly
equally spaced, along the polypeptide chain. The folded protein brings these motifs close to each
other at the catalytic center between an all- domain and an / domain.[9][10][11]
The structure of the streptomyces K15 DD-transpeptidase has been studied , and consists of a
single polypeptide chain organized into two domains. One domain contains mainly -helices, and
the second one is of /-type.[6] The center of the catalytic cleft is occupied by the Ser35-Thr36-
Thr37-Lys38 tetrad, which includes the nucleophilic Ser35 residue at the amino-terminal end of
helix 2. One side of the cavity is defined by the Ser96-Gly97-Cys98 loop connecting helices 4
and 5. The Lys213-Thr214-Gly215 triad lies on strand 3 on the opposite side of the cavity. The
backbone NH group of the essential Ser35 residue and that of Ser216 downstream from the
motif Lys213-Thr214-Gly215 occupy positions that are compatible with the oxyanion
hole function required for catalysis.[6]
The enzyme is classified as a DD-transpeptidase because the susceptible peptide bond of the
carbonyl donor extends between two carbon atoms with the D-configuration. [6]

Biological Function[edit]
All bacteria possess at least one, most often several, monofunctional serine DD-peptidases. [2]

Disease Relevance[edit]

The structural similarity between (A) D-Ala-D-Ala terminus of peptidoglycan terminus and (B) penicillins.
Transpeptidases misrecognize penicillins for the TPase catalytic reaction.
This enzyme is an excellent drug target because it is essential, is accessible from the periplasm,
and has no equivalent in mammalian cells. DD-transpeptidase is the target protein of the
famous -lactam antibiotics. This is because the structure of the -lactam closely resembles the
D-ala-D-ala residue.
Penicillins exert their effect by competitively inactivating the serine DD-transpeptidase catalytic
site. Penicillin is a cyclic analogue of the D-Ala-D-Ala terminated carbonyl donors, therefore in
the presence of this antibiotic, the reaction stops at the level of the serine ester-linked penicilloyl
enzyme.[12] Thus -lactam antibiotics force these enzymes to behave like penicillin binding
proteins.[13]
Kinetically, the interaction between the DD-peptidase and beta-lactams is a three-step reaction:
[13]

Beta-Iactams may form an adduct E-I* of high stability with DD-transpeptidase. The half life of
this adduct is around hours, whereas the half-life of the normal reaction is in the order of
milliseconds.[8]
The interference with the enzyme processes responsible for cell wall formation results in cellular
lysis and death due to the triggering of the autolytic system in the bacteria. [14]