PDBsum entry: 1m1z

Hydrolase

PDB id: 1m1z

Contents

Protein chains

480 a.a. *

Waters ×603

* Residue conservation analysis

PDB id:

1m1z

Name:

Hydrolase

Title:

Beta-lactam synthetase apo enzyme

Structure:

Beta-lactam synthetase. Chain: a, b. Engineered: yes

Source:

Streptomyces clavuligerus. Organism_taxid: 1901. Gene: taxon:1901. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.95Å R-factor: 0.197 R-free: 0.231

Authors:

M.T.Miller,B.O.Bachmann,C.A.Townsend,A.C.Rosenzweig

Key ref:

M.T.Miller et al. (2002). The catalytic cycle of beta -lactam synthetase observed by x-ray crystallographic snapshots. Proc Natl Acad Sci U S A, 99, 14752-14757. PubMed id: 12409610 DOI: 10.1073/pnas.232361199

Date:

20-Jun-02 Release date: 23-Oct-02

Protein chains

Q9R8E3  (BLS_STRCL) -  Carboxyethyl-arginine beta-lactam-synthase

Seq: 513 a.a.

Struc: 480 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.3.4 - (Carboxyethyl)arginine beta-lactam-synthase.
• Pathway: Clavulanate Biosynthesis
• Reaction: ATP + L-N₂-(2-carboxyethyl)arginine = AMP + diphosphate + deoxyamidinoproclavaminate

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

 Gene Ontology (GO) functional annotation 

• Biological process: asparagine biosynthetic process (1 term)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1073/pnas.232361199

Proc Natl Acad Sci U S A 99:14752-14757 (2002)

PubMed id: 12409610

The catalytic cycle of beta -lactam synthetase observed by x-ray crystallographic snapshots.

M.T.Miller, B.O.Bachmann, C.A.Townsend, A.C.Rosenzweig.

ABSTRACT

The catalytic cycle of the ATP/Mg(2+)-dependent enzyme beta-lactam synthetase (beta-LS) from Streptomyces clavuligerus has been observed through a series of x-ray crystallographic snapshots. Chemistry is initiated by the ordered binding of ATP/Mg(2+) and N(2)-(carboxyethyl)-l-arginine (CEA) to the apoenzyme. The apo and ATP/Mg(2+) structures described here, along with the previously described CEA.alpha,beta-methyleneadenosine 5'-triphosphate (CEA.AMP-CPP)/Mg(2+) structure, illuminate changes in active site geometry that favor adenylation. In addition, an acyladenylate intermediate has been trapped. The substrate analog N(2)-(carboxymethyl)-l-arginine (CMA) was adenylated by ATP in the crystal and represents a close structural analog of the previously proposed CEA-adenylate intermediate. Finally, the structure of the ternary product complex deoxyguanidinoproclavaminic acid (DGPC).AMP/PP(i)/Mg(2+) has been determined. The CMA-AMP/PP(i)/Mg(2+) and DGPC.AMP/PP(i)/Mg(2+) structures reveal interactions in the active site that facilitate beta-lactam formation. All of the ATP-bound structures differ from the previously described CEA.AMP-CPP/Mg(2+) structure in that two Mg(2+) ions are found in the active sites. These Mg(2+) ions play critical roles in both the adenylation and beta-lactamization reactions.

Selected figure(s)

Figure 4.
Fig 4. Mechanistically important hydrogen bonding interactions in the CMA-AMP/PP[i]/Mg2+ active site. The conformations of Tyr-326, Tyr-348, and Lys-443 differ from those observed in the apo structure (superimposed in green).

Figure 5.
Fig 5. Chemical mechanism of -LS based on structural and kinetic data.

Figures were selected by an automated process.