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PDBsum entry 1jtd
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protein metals Protein-protein interface(s) links
Hydrolase/inhibitor PDB id
1jtd

 

 

 

 

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Contents
Protein chains
262 a.a. *
273 a.a. *
Metals
_CA ×5
Waters ×366
* Residue conservation analysis
PDB id:
1jtd
Name: Hydrolase/inhibitor
Title: Crystal structure of beta-lactamase inhibitor protein-ii in complex with tem-1 beta-lactamase
Structure: Tem-1 beta-lactamase. Chain: a. Engineered: yes. Beta-lactamase inhibitor protein ii. Chain: b
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Streptomyces exfoliatus. Organism_taxid: 1905. Strain: smf19
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.178     R-free:   0.230
Authors: D.C.Lim,H.U.Park,L.De Castro,S.G.Kang,H.S.Lee,S.Jensen,K.J.Lee, N.C.J.Strynadka
Key ref:
D.Lim et al. (2001). Crystal structure and kinetic analysis of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase. Nat Struct Biol, 8, 848-852. PubMed id: 11573088 DOI: 10.1038/nsb1001-848
Date:
20-Aug-01     Release date:   03-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62593  (BLAT_ECOLX) -  Beta-lactamase TEM from Escherichia coli
Seq:
Struc: 		286 a.a.
262 a.a.*
Protein chain
Pfam   ArchSchema ?
O87916  (O87916_STREX) -  Beta-lactamase inhibitory protein II from Streptomyces exfoliatus
Seq:
Struc: 		311 a.a.
273 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.3.5.2.6  - beta-lactamase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Penicillin Biosynthesis and Metabolism
      Reaction: a beta-lactam + H2O = a substituted beta-amino acid
      Cofactor: Zn(2+)

 

 
DOI no: 10.1038/nsb1001-848 Nat Struct Biol 8:848-852 (2001)
PubMed id: 11573088  
 
 
Crystal structure and kinetic analysis of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase.
D.Lim, H.U.Park, L.De Castro, S.G.Kang, H.S.Lee, S.Jensen, K.J.Lee, N.C.Strynadka.
 
  ABSTRACT  
 
The structure of the 28 kDa beta-lactamase inhibitor protein-II (BLIP-II) in complex with the TEM-1 beta-lactamase has been determined to 2.3 A resolution. BLIP-II is a secreted protein produced by the soil bacterium Streptomyces exfoliatus SMF19 and is able to bind and inhibit TEM-1 with subnanomolar affinity. BLIP-II is a seven-bladed beta-propeller with a unique blade motif consisting of only three antiparallel beta-strands. The overall fold is highly similar to the core structure of the human regulator of chromosome condensation (RCC1). Although BLIP-II does not share the same fold with BLIP, the first beta-lactamase inhibitor protein for which structural data was available, a comparison of the two complexes reveals a number of similarities and provides further insights into key components of the TEM-1-BLIP and TEM-1-BLIP-II interfaces. Our preliminary results from gene knock-out studies and scanning electron microscopy also reveal a critical role of BLIP-II in sporulation.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. TEM-1 -BLIP interface. a, BLIP (blue) binds competitively to TEM-1 (orange). BLIP has an overall -saddle fold consisting of two tandem repeats. The large concave eight-stranded -sheet of BLIP wraps around the TEM-1 loop-helix region (green). Asp 49 and Phe 142 on the protruding -hairpin turns of BLIP insert into the TEM-1 active site cavity and structurally mimic the carboxylate and benzyl side chain of a penicillin substrate. To illustrate the competitive mode of inhibition, the penicilloyl moiety (thin stick rendering) of the TEM-1 -penicillin G acyl-enzyme intermediate^13 is superimposed on the active site region of the complex. b, Interface between BLIP (blue) and the TEM-1 loop-helix region (residues 99 -114 shown in stick rendering with green carbons). For clarity, the side chains of Asp 101, Thr 109 and His 112 on TEM-1 were omitted. 		Figure 4.
Figure 4. Scanning electron micrographs of Streptomyces exfoliatus SMF19 cells. a, Spore formation by septation of wild type hyphae. b, The absence of sporulation in a BLIP-II knock-out mutant produces the so-called 'bald' phenotype. c, Comparison of the structures of TEM-1 -lactamase (orange) and the Streptomyces K15 penicillin binding protein (K15 PBP)30 (blue), highlighting the overall structural similarities. The region in TEM-1 to which BLIP-II binds is colored green, as is the structurally equivalent region in the K15 PBP. The active site Ser-Lys dyads are shown as ball-and-stick renderings.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 848-852) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21354429 A.M.Ruvinsky, T.Kirys, A.V.Tuzikov, and I.A.Vakser (2011).
Side-chain conformational changes upon Protein-Protein Association.
  J Mol Biol, 408, 356-365.  
21071205 G.Schreiber, and A.E.Keating (2011).
Protein binding specificity versus promiscuity.
  Curr Opin Struct Biol, 21, 50-61.  
21097468 J.Segura, and N.Fernandez-Fuentes (2011).
PCRPi-DB: a database of computationally annotated hot spots in protein interfaces.
  Nucleic Acids Res, 39, D755-D760.  
21168530 L.Mathieu, S.Marsy, Y.Saint-Georges, C.Jacq, and G.Dujardin (2011).
A transcriptome screen in yeast identifies a novel assembly factor for the mitochondrial complex III.
  Mitochondrion, 11, 391-396.  
20544968 D.J.Diller, C.Humblet, X.Zhang, and L.M.Westerhoff (2010).
Computational alanine scanning with linear scaling semiempirical quantum mechanical methods.
  Proteins, 78, 2329-2337.  
20308189 N.G.Brown, and T.Palzkill (2010).
Identification and characterization of beta-lactamase inhibitor protein-II (BLIP-II) interactions with beta-lactamases using phage display.
  Protein Eng Des Sel, 23, 469-478.  
19023603 D.C.Soares, P.N.Barlow, D.J.Porteous, and R.S.Devon (2009).
An interrupted beta-propeller and protein disorder: structural bioinformatics insights into the N-terminus of alsin.
  J Mol Model, 15, 113-122.  
19450494 M.Harel, A.Spaar, and G.Schreiber (2009).
Fruitful and futile encounters along the association reaction between proteins.
  Biophys J, 96, 4237-4248.  
18186471 M.M.Vanini, A.Spisni, M.L.Sforça, T.A.Pertinhez, and C.E.Benedetti (2008).
The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein-protein interaction.
  Proteins, 71, 2051-2064.
PDB code: 2pxg
17680689 T.J.Stevens, and M.Paoli (2008).
RCC1-like repeat proteins: a pangenomic, structurally diverse new superfamily of beta-propeller domains.
  Proteins, 70, 378-387.  
18069884 A.Del Sol, and P.Carbonell (2007).
The Modular Organization of Domain Structures: Insights into Protein-Protein Binding.
  PLoS Comput Biol, 3, e239.  
17600829 N.Doucet, and J.N.Pelletier (2007).
Simulated annealing exploration of an active-site tyrosine in TEM-1 beta-lactamase suggests the existence of alternate conformations.
  Proteins, 69, 340-348.  
17008715 A.Ertekin, R.Nussinov, and T.Haliloglu (2006).
Association of putative concave protein-binding sites with the fluctuation behavior of residues.
  Protein Sci, 15, 2265-2277.  
15987886 M.Jäger, X.Michalet, and S.Weiss (2005).
Protein-protein interactions as a tool for site-specific labeling of proteins.
  Protein Sci, 14, 2059-2068.  
15549374 X.Cao, K.Li, S.G.Suh, T.Guo, and P.W.Becraft (2005).
Molecular analysis of the CRINKLY4 gene family in Arabidopsis thaliana.
  Planta, 220, 645-657.  
11937049 Z.Jawad, and M.Paoli (2002).
Novel sequences propel familiar folds.
  Structure, 10, 447-454.  
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 code is shown on the right.

 

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