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PDBsum entry 1vm1
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Hydrolase PDB id
1vm1

 

 

 

 

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Contents
Protein chain
265 a.a. *
Ligands
MA4 ×2
TBE
AKR
TAZ
Waters ×175
* Residue conservation analysis
PDB id:
1vm1
Name: Hydrolase
Title: Structure of shv-1 beta-lactamase inhibited by tazobactam
Structure: Beta-lactamase shv-1. Chain: a. Engineered: yes
Source: Klebsiella pneumoniae. Organism_taxid: 573. Gene: bla. Expressed in: escherichia coli str. K-12 substr. Dh10b. Expression_system_taxid: 316385.
Resolution:
2.02Å     R-factor:   0.177     R-free:   0.257
Authors: A.P.Kuzin,M.Nukaga,Y.Nukaga,A.Hujer,R.A.Bonomo,J.R.Knox
Key ref:
A.P.Kuzin et al. (2001). Inhibition of the SHV-1 beta-lactamase by sulfones: crystallographic observation of two reaction intermediates with tazobactam. Biochemistry, 40, 1861-1866. PubMed id: 11327849 DOI: 10.1021/bi0022745
Date:
27-Aug-04     Release date:   07-Sep-04    
Supersedes: 1g56
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P0AD64  (BLA1_KLEPN) -  Beta-lactamase SHV-1 from Klebsiella pneumoniae
Seq:
Struc: 		286 a.a.
265 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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: 10.1021/bi0022745 Biochemistry 40:1861-1866 (2001)
PubMed id: 11327849  
 
 
Inhibition of the SHV-1 beta-lactamase by sulfones: crystallographic observation of two reaction intermediates with tazobactam.
A.P.Kuzin, M.Nukaga, Y.Nukaga, A.Hujer, R.A.Bonomo, J.R.Knox.
 
  ABSTRACT  
 
Two species resulting from the reaction of the SHV-1 class A beta-lactamase with the sulfone inhibitor tazobactam have been trapped at 100 K and mapped by X-ray crystallography at 2.0 A resolution. An acyclic form of tazobactam is covalently bonded to the catalytic Ser70 side chain, and a second species, a five-atom vinyl carboxylic acid fragment of tazobactam, is bonded to Ser130. It is proposed that the electron density map of the crystal is a composite picture of two complexes, each with only a single bound species. It is estimated that the two complexes exist in the crystal in approximately equal populations. Results are discussed in relation to the mechanism-based inhibition of class A beta-lactamases by the similar inhibitors sulbactam and clavulanic acid.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20457000 A.F.Kluge, and R.C.Petter (2010).
Acylating drugs: redesigning natural covalent inhibitors.
  Curr Opin Chem Biol, 14, 421-427.  
20065329 S.M.Drawz, and R.A.Bonomo (2010).
Three decades of beta-lactamase inhibitors.
  Clin Microbiol Rev, 23, 160-201.  
19919161 E.Sauvage, A.Zervosen, G.Dive, R.Herman, A.Amoroso, B.Joris, E.Fonzé, R.F.Pratt, A.Luxen, P.Charlier, and F.Kerff (2009).
Structural basis of the inhibition of class A beta-lactamases and penicillin-binding proteins by 6-beta-iodopenicillanate.
  J Am Chem Soc, 131, 15262-15269.
PDB codes: 2wk0 2wke
19161282 M.Kalp, M.A.Totir, J.D.Buynak, and P.R.Carey (2009).
Different intermediate populations formed by tazobactam, sulbactam, and clavulanate reacting with SHV-1 beta-lactamases: Raman crystallographic evidence.
  J Am Chem Soc, 131, 2338-2347.  
18955486 P.Pattanaik, C.R.Bethel, A.M.Hujer, K.M.Hujer, A.M.Distler, M.Taracila, V.E.Anderson, T.R.Fritsche, R.N.Jones, S.R.Pagadala, F.van den Akker, J.D.Buynak, and R.A.Bonomo (2009).
Strategic design of an effective beta-lactamase inhibitor: LN-1-255, a 6-alkylidene-2'-substituted penicillin sulfone.
  J Biol Chem, 284, 945-953.
PDB code: 3d4f
18559643 C.R.Bethel, A.M.Distler, M.W.Ruszczycky, M.P.Carey, P.R.Carey, A.M.Hujer, M.Taracila, M.S.Helfand, J.M.Thomson, M.Kalp, V.E.Anderson, D.A.Leonard, K.M.Hujer, T.Abe, A.M.Venkatesan, T.S.Mansour, and R.A.Bonomo (2008).
Inhibition of OXA-1 beta-lactamase by penems.
  Antimicrob Agents Chemother, 52, 3135-3143.  
18019537 J.Mulchande, L.Martins, R.Moreira, M.Archer, T.F.Oliveira, and J.Iley (2007).
The efficiency of C-4 substituents in activating the beta-lactam scaffold towards serine proteases and hydroxide ion.
  Org Biomol Chem, 5, 2617-2626.
PDB code: 2v35
17630699 M.A.Totir, M.S.Helfand, M.P.Carey, A.Sheri, J.D.Buynak, R.A.Bonomo, and P.R.Carey (2007).
Sulbactam forms only minimal amounts of irreversible acrylate-enzyme with SHV-1 beta-lactamase.
  Biochemistry, 46, 8980-8987.  
17207608 Y.Ishii, M.Galleni, L.Ma, J.M.Frère, and K.Yamaguchi (2007).
Biochemical characterisation of the CTX-M-14 beta-lactamase.
  Int J Antimicrob Agents, 29, 159-164.  
16870770 F.Wang, C.Cassidy, and J.C.Sacchettini (2006).
Crystal structure and activity studies of the Mycobacterium tuberculosis beta-lactamase reveal its critical role in resistance to beta-lactam antibiotics.
  Antimicrob Agents Chemother, 50, 2762-2771.
PDB code: 2gdn
17002290 M.A.Totir, P.S.Padayatti, M.S.Helfand, M.P.Carey, R.A.Bonomo, P.R.Carey, and F.van den Akker (2006).
Effect of the inhibitor-resistant M69V substitution on the structures and populations of trans-enamine beta-lactamase intermediates.
  Biochemistry, 45, 11895-11904.
PDB codes: 2h0t 2h0y 2h10
17017804 P.S.Padayatti, A.Sheri, M.A.Totir, M.S.Helfand, M.P.Carey, V.E.Anderson, P.R.Carey, C.R.Bethel, R.A.Bonomo, J.D.Buynak, and F.van den Akker (2006).
Rational design of a beta-lactamase inhibitor achieved via stabilization of the trans-enamine intermediate: 1.28 A crystal structure of wt SHV-1 complex with a penam sulfone.
  J Am Chem Soc, 128, 13235-13242.
PDB code: 2h5s
15987690 D.Sulton, D.Pagan-Rodriguez, X.Zhou, Y.Liu, A.M.Hujer, C.R.Bethel, M.S.Helfand, J.M.Thomson, V.E.Anderson, J.D.Buynak, L.M.Ng, and R.A.Bonomo (2005).
Clavulanic acid inactivation of SHV-1 and the inhibitor-resistant S130G SHV-1 beta-lactamase. Insights into the mechanism of inhibition.
  J Biol Chem, 280, 35528-35536.  
15673739 L.Ma, J.Alba, F.Y.Chang, M.Ishiguro, K.Yamaguchi, L.K.Siu, and Y.Ishii (2005).
Novel SHV-derived extended-spectrum beta-lactamase, SHV-57, that confers resistance to ceftazidime but not cefazolin.
  Antimicrob Agents Chemother, 49, 600-605.  
16055923 P.S.Padayatti, M.S.Helfand, M.A.Totir, M.P.Carey, P.R.Carey, R.A.Bonomo, and F.van den Akker (2005).
High resolution crystal structures of the trans-enamine intermediates formed by sulbactam and clavulanic acid and E166A SHV-1 {beta}-lactamase.
  J Biol Chem, 280, 34900-34907.
PDB codes: 2a3u 2a49
15981999 V.L.Thomas, D.Golemi-Kotra, C.Kim, S.B.Vakulenko, S.Mobashery, and B.K.Shoichet (2005).
Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase.
  Biochemistry, 44, 9330-9338.
PDB code: 1yt4
14757767 D.Pagan-Rodriguez, X.Zhou, R.Simmons, C.R.Bethel, A.M.Hujer, M.S.Helfand, Z.Jin, B.Guo, V.E.Anderson, L.M.Ng, and R.A.Bonomo (2004).
Tazobactam inactivation of SHV-1 and the inhibitor-resistant Ser130 -->Gly SHV-1 beta-lactamase: insights into the mechanism of inhibition.
  J Biol Chem, 279, 19494-19501.  
15561830 W.J.Weiss, P.J.Petersen, T.M.Murphy, L.Tardio, Y.Yang, P.A.Bradford, A.M.Venkatesan, T.Abe, T.Isoda, A.Mihira, H.Ushirogochi, T.Takasake, S.Projan, J.O'Connell, and T.S.Mansour (2004).
In vitro and in vivo activities of novel 6-methylidene penems as beta-lactamase inhibitors.
  Antimicrob Agents Chemother, 48, 4589-4596.  
14757816 Y.Bourne, H.C.Kolb, Z.Radić, K.B.Sharpless, P.Taylor, and P.Marchot (2004).
Freeze-frame inhibitor captures acetylcholinesterase in a unique conformation.
  Proc Natl Acad Sci U S A, 101, 1449-1454.
PDB codes: 1q83 1q84
14534312 M.S.Helfand, C.R.Bethel, A.M.Hujer, K.M.Hujer, V.E.Anderson, and R.A.Bonomo (2003).
Understanding resistance to beta-lactams and beta-lactamase inhibitors in the SHV beta-lactamase: lessons from the mutagenesis of SER-130.
  J Biol Chem, 278, 52724-52729.  
14621983 M.S.Helfand, M.A.Totir, M.P.Carey, A.M.Hujer, R.A.Bonomo, and P.R.Carey (2003).
Following the reactions of mechanism-based inhibitors with beta-lactamase by Raman crystallography.
  Biochemistry, 42, 13386-13392.  
12354765 M.S.Helfand, A.M.Hujer, F.D.Sönnichsen, and R.A.Bonomo (2002).
Unexpected advanced generation cephalosporinase activity of the M69F variant of SHV beta-lactamase.
  J Biol Chem, 277, 47719-47723.  
12058046 X.Wang, G.Minasov, and B.K.Shoichet (2002).
The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34.
  J Biol Chem, 277, 32149-32156.
PDB codes: 1lhy 1li0 1li9
11478888 R.A.Powers, E.Caselli, P.J.Focia, F.Prati, and B.K.Shoichet (2001).
Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design.
  Biochemistry, 40, 9207-9214.
PDB codes: 1iel 1iem
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.

 

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