4IVK

Crystal structure of a fammily VIII carboxylesterase in a complex with cephalothin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the beta-lactamase activity of EstU1, a family VIII carboxylesterase.

Cha, S.S.An, Y.J.Jeong, C.S.Kim, M.K.Jeon, J.H.Lee, C.M.Lee, H.S.Kang, S.G.Lee, J.H.

(2013) Proteins 81: 2045-2051

  • DOI: 10.1002/prot.24334
  • Primary Citation of Related Structures:  
    4IVI, 4IVK

  • PubMed Abstract: 
  • EstU1 is a unique family VIII carboxylesterase that displays hydrolytic activity toward the amide bond of clinically used β-lactam antibiotics as well as the ester bond of p-nitrophenyl esters. EstU1 assumes a β-lactamase-like modular architecture and contains the residues Ser100, Lys103, and Tyr218, which correspond to the three catalytic residues (Ser64, Lys67, and Tyr150, respectively) of class C β-lactamases ...

    EstU1 is a unique family VIII carboxylesterase that displays hydrolytic activity toward the amide bond of clinically used β-lactam antibiotics as well as the ester bond of p-nitrophenyl esters. EstU1 assumes a β-lactamase-like modular architecture and contains the residues Ser100, Lys103, and Tyr218, which correspond to the three catalytic residues (Ser64, Lys67, and Tyr150, respectively) of class C β-lactamases. The structure of the EstU1/cephalothin complex demonstrates that the active site of EstU1 is not ideally tailored to perform an efficient deacylation reaction during the hydrolysis of β-lactam antibiotics. This result explains the weak β-lactamase activity of EstU1 compared with class C β-lactamases. Finally, structural and sequential comparison of EstU1 with other family VIII carboxylesterases elucidates an operative molecular strategy used by family VIII carboxylesterases to extend their substrate spectrum.


    Organizational Affiliation

    Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan, 426-744, Republic of Korea; Ocean Science and Technology School, Korea Maritime University, Pusan, 606-791, Republic of Korea; Department of Marine Biotechnology, University of Science and Technology, Daejeon, 305-333, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CarboxylesterasesA434uncultured bacteriumMutation(s): 0 
EC: 3.1.1.1
UniProt
Find proteins for K4HQE7 (uncultured bacterium)
Explore K4HQE7 
Go to UniProtKB:  K4HQE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK4HQE7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CEP
Query on CEP

Download Ideal Coordinates CCD File 
B [auth A]CEPHALOTHIN GROUP
C16 H18 N2 O6 S2
UUWFGEKEQSCSMB-IAQYHMDHSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CEP PDBBind:  4IVK Ki: 1.40e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.102α = 90
b = 149.102β = 90
c = 172.571γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references