3M81

Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTOGA MARITIMA at 2.50 A resolution (native apo structure)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 3.1.1.72 (UniProt), 3.1.1.41 (UniProt)
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
K [auth A]
L [auth A]
O [auth B]
AA [auth E],
DA [auth F],
K [auth A],
L [auth A],
O [auth B],
R [auth C],
W [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
J [auth A],
V [auth D],
Z [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth F]
G [auth A]
H [auth A]
M [auth B]
P [auth C]
BA [auth F],
G [auth A],
H [auth A],
M [auth B],
P [auth C],
S [auth D],
T [auth D],
X [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth F]
I [auth A]
N [auth B]
Q [auth C]
U [auth D]
CA [auth F],
I [auth A],
N [auth B],
Q [auth C],
U [auth D],
Y [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.46α = 90
b = 103.79β = 90
c = 221.02γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PHASERphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-21
    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, Refinement description
  • Version 1.6: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.7: 2023-09-20
    Changes: Data collection, Refinement description