Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTOGA MARITIMA at 2.40 A resolution (PMSF inhibitor complex structure)

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report

This is version 1.7 of the entry. See complete history


Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima.

Levisson, M.Han, G.W.Deller, M.C.Xu, Q.Biely, P.Hendriks, S.Ten Eyck, L.F.Flensburg, C.Roversi, P.Miller, M.D.McMullan, D.von Delft, F.Kreusch, A.Deacon, A.M.van der Oost, J.Lesley, S.A.Elsliger, M.A.Kengen, S.W.Wilson, I.A.

(2012) Proteins 80: 1545-1559

  • DOI: https://doi.org/10.1002/prot.24041
  • Primary Citation of Related Structures:  
    1VLQ, 3M81, 3M82, 3M83

  • PubMed Abstract: 

    TM0077 from Thermotoga maritima is a member of the carbohydrate esterase family 7 and is active on a variety of acetylated compounds, including cephalosporin C. TM0077 esterase activity is confined to short-chain acyl esters (C2-C3), and is optimal around 100°C and pH 7.5. The positional specificity of TM0077 was investigated using 4-nitrophenyl-β-D-xylopyranoside monoacetates as substrates in a β-xylosidase-coupled assay. TM0077 hydrolyzes acetate at positions 2, 3, and 4 with equal efficiency. No activity was detected on xylan or acetylated xylan, which implies that TM0077 is an acetyl esterase and not an acetyl xylan esterase as currently annotated. Selenomethionine-substituted and native structures of TM0077 were determined at 2.1 and 2.5 Å resolution, respectively, revealing a classic α/β-hydrolase fold. TM0077 assembles into a doughnut-shaped hexamer with small tunnels on either side leading to an inner cavity, which contains the six catalytic centers. Structures of TM0077 with covalently bound phenylmethylsulfonyl fluoride and paraoxon were determined to 2.4 and 2.1 Å, respectively, and confirmed that both inhibitors bind covalently to the catalytic serine (Ser188). Upon binding of inhibitor, the catalytic serine adopts an altered conformation, as observed in other esterase and lipases, and supports a previously proposed catalytic mechanism in which Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction.

  • Organizational Affiliation

    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl xylan esterase
A, B, C, D, E
A, B, C, D, E, F
337Thermotoga maritimaMutation(s): 0 
Gene Names: TM0077TM_0077
Find proteins for Q9WXT2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WXT2 
Go to UniProtKB:  Q9WXT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WXT2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
N [auth B]
P [auth C]
U [auth E]
J [auth A],
K [auth A],
N [auth B],
P [auth C],
U [auth E],
W [auth F]
C2 H6 O2
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
T [auth E]
C2 H3 O2
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
L [auth B]
O [auth C]
Q [auth D]
G [auth A],
H [auth A],
L [auth B],
O [auth C],
Q [auth D],
R [auth D],
S [auth E],
V [auth F]
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on SEB
A, B, C, D, E
A, B, C, D, E, F
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.57α = 90
b = 104.5β = 90
c = 221.61γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-09
    Changes: Database references
  • Version 1.3: 2013-01-09
    Changes: Database references
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.5: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.6: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.7: 2023-09-20
    Changes: Data collection, Refinement description