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PDBsum entry 1mb9

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1mb9
Jmol
Contents
Protein chains
485 a.a. *
Ligands
POP
AMP
ATP ×2
Metals
_MG ×4
Waters ×470
* Residue conservation analysis
PDB id:
1mb9
Name: Hydrolase
Title: Beta-lactam synthetase complexed with atp
Structure: Beta-lactam synthetase. Chain: a, b. Engineered: yes
Source: Streptomyces clavuligerus. Organism_taxid: 1901. Gene: 1901. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.11Å     R-factor:   0.210     R-free:   0.251
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:
02-Aug-02     Release date:   23-Oct-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P0DJQ7  (BLS_STRCL) -  Carboxyethyl-arginine beta-lactam-synthase
Seq:
Struc:
513 a.a.
485 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.3.4  - (Carboxyethyl)arginine beta-lactam-synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Clavulanate Biosynthesis
      Reaction: ATP + L-N2-(2-carboxyethyl)arginine = AMP + diphosphate + deoxyamidinoproclavaminate
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+ L-N(2)-(2-carboxyethyl)arginine
=
AMP
Bound ligand (Het Group name = AMP)
corresponds exactly
+
diphosphate
Bound ligand (Het Group name = POP)
corresponds exactly
+ deoxyamidinoproclavaminate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20711575 J.Y.Song, S.E.Jensen, and K.J.Lee (2010).
Clavulanic acid biosynthesis and genetic manipulation for its overproduction.
  Appl Microbiol Biotechnol, 88, 659-669.  
19604476 E.E.Chufán, M.De, B.A.Eipper, R.E.Mains, and L.M.Amzel (2009).
Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme.
  Structure, 17, 965-973.
PDB codes: 3fvz 3fw0
19882698 M.L.Raber, A.Castillo, A.Greer, and C.A.Townsend (2009).
A conserved lysine in beta-lactam synthetase assists ring cyclization: Implications for clavam and carbapenem biosynthesis.
  Chembiochem, 10, 2904-2912.  
18955494 M.L.Raber, M.F.Freeman, and C.A.Townsend (2009).
Dissection of the stepwise mechanism to beta-lactam formation and elucidation of a rate-determining conformational change in beta-lactam synthetase.
  J Biol Chem, 284, 207-217.  
19371088 M.L.Raber, S.O.Arnett, and C.A.Townsend (2009).
A conserved tyrosyl-glutamyl catalytic dyad in evolutionarily linked enzymes: carbapenam synthetase and beta-lactam synthetase.
  Biochemistry, 48, 4959-4971.  
19726666 S.K.Lim, J.Ju, E.Zazopoulos, H.Jiang, J.W.Seo, Y.Chen, Z.Feng, S.R.Rajski, C.M.Farnet, and B.Shen (2009).
iso-Migrastatin, migrastatin, and dorrigocin production in Streptomyces platensis NRRL 18993 is governed by a single biosynthetic machinery featuring an acyltransferase-less type I polyketide synthase.
  J Biol Chem, 284, 29746-29756.  
17711420 K.Severinov, E.Semenova, A.Kazakov, T.Kazakov, and M.S.Gelfand (2007).
Low-molecular-weight post-translationally modified microcins.
  Mol Microbiol, 65, 1380-1394.  
17656316 S.Duquesne, D.Destoumieux-Garzón, S.Zirah, C.Goulard, J.Peduzzi, and S.Rebuffat (2007).
Two enzymes catalyze the maturation of a lasso peptide in Escherichia coli.
  Chem Biol, 14, 793-803.  
16756505 N.G.Richards, and M.S.Kilberg (2006).
Asparagine synthetase chemotherapy.
  Annu Rev Biochem, 75, 629-654.  
16129597 D.Bourgeois, and A.Royant (2005).
Advances in kinetic protein crystallography.
  Curr Opin Struct Biol, 15, 538-547.  
16113715 N.J.Kershaw, M.E.Caines, M.C.Sleeman, and C.J.Schofield (2005).
The enzymology of clavam and carbapenem biosynthesis.
  Chem Commun (Camb), (), 4251-4263.  
15759042 S.J.Coulthurst, A.M.Barnard, and G.P.Salmond (2005).
Regulation and biosynthesis of carbapenem antibiotics in bacteria.
  Nat Rev Microbiol, 3, 295-306.  
14982786 K.Tahlan, H.U.Park, A.Wong, P.H.Beatty, and S.E.Jensen (2004).
Two sets of paralogous genes encode the enzymes involved in the early stages of clavulanic acid and clavam metabolite biosynthesis in Streptomyces clavuligerus.
  Antimicrob Agents Chemother, 48, 930-939.  
15150229 L.M.Lorenzana, R.Pérez-Redondo, I.Santamarta, J.F.Martín, and P.Liras (2004).
Two oligopeptide-permease-encoding genes in the clavulanic acid cluster of Streptomyces clavuligerus are essential for production of the beta-lactamase inhibitor.
  J Bacteriol, 186, 3431-3438.  
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.