 |
PDBsum entry 1k17
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Support for a three-Dimensional structure predicting a cys-Glu-Lys catalytic triad for pseudomonas aeruginosa amidase comes from site-Directed mutagenesis and mutations altering substrate specificity.
|
|
|
Authors
|
|
C.Novo,
S.Farnaud,
R.Tata,
A.Clemente,
P.R.Brown.
|
|
|
Ref.
|
|
Biochem J, 2002,
365,
731-738.
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The aliphatic amidase from Pseudomonas aeruginosa belongs to the nitrilase
superfamily, and Cys(166) is the nucleophile of the catalytic mechanism. A model
of amidase was built by comparative modelling using the crystal structure of the
worm nitrilase-fragile histidine triad fusion protein (NitFhit; Protein Data
Bank accession number 1EMS) as a template. The amidase model predicted a
catalytic triad (Cys-Glu-Lys) situated at the bottom of a pocket and identical
with the presumptive catalytic triad of NitFhit. Three-dimensional models for
other amidases belonging to the nitrilase superfamily also predicted Cys-Glu-Lys
catalytic triads. Support for the structure for the P. aeruginosa amidase came
from site-direct mutagenesis and from the locations of amino acid residues that
altered substrate specificity or binding when mutated.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Protein modeling by email
|
|
|
Author
|
|
M.C.Peitsch.
|
|
|
Ref.
|
|
biotechnology, 1995,
13,
658.
|
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Promod and swiss-Model: internet-Based tools for automated comparative protein modelling.
|
|
|
Author
|
|
M.C.Peitsch.
|
|
|
Ref.
|
|
Biochem Soc Trans, 1996,
24,
274-279.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #3
|
|
|
Title
|
|
Large-Scale comparative protein modelling
|
|
|
Authors
|
|
M.C.Peitsch,
N.Guex.
|
|
|
Ref.
|
|
proteome research: new, 1997,
19,
177.
|
|
|
|
Secondary reference #4
|
|
|
Title
|
|
Swiss-Model and the swiss-Pdbviewer: an environment for comparative protein modeling.
|
|
|
Authors
|
|
N.Guex,
M.C.Peitsch.
|
|
|
Ref.
|
|
Electrophoresis, 1997,
18,
2714-2723.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #5
|
|
|
Title
|
|
A computer modeling study of the interaction between tissue factor pathway inhibitor and blood coagulation factor xa.
|
|
|
Authors
|
|
T.Yoneda,
H.Komooka,
H.Umeyama.
|
|
|
Ref.
|
|
J Protein Chem, 1997,
16,
597-605.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #6
|
|
|
Title
|
|
Prediction of protein side-Chain conformations by principal component analysis for fixed main-Chain atoms.
|
|
|
Authors
|
|
K.Ogata,
H.Umeyama.
|
|
|
Ref.
|
|
Protein Eng, 1997,
10,
353-359.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #7
|
|
|
Title
|
|
The role played by environmental residues on sidechain torsional angles within homologous families of proteins: a new method of sidechain modeling.
|
|
|
Authors
|
|
K.Ogata,
H.Umeyama.
|
|
|
Ref.
|
|
Proteins, 1998,
31,
355-369.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #8
|
|
|
Title
|
|
Crystal structure of the worm nitfhit rosetta stone protein reveals a nit tetramer binding two fhit dimers.
|
|
|
Authors
|
|
H.C.Pace,
S.C.Hodawadekar,
A.Draganescu,
J.Huang,
P.Bieganowski,
Y.Pekarsky,
C.M.Croce,
C.Brenner.
|
|
|
Ref.
|
|
Curr Biol, 2000,
10,
907-917.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 2.
Structure determination of NitFhit. (a) A portion of the 2.8
Å experimental electron density map in stereo. The map
was contoured at 1.5 σ and superimposed on the refined atomic
model. (b) Stereo ribbon view of the Nit domain of a NitFhit
monomer (northern conformation). Secondary structural elements
are indicated. The Fhit domain, carboxy terminal to the Nit
domain, and three additional subunits of the NitFhit tetramer
are not shown. N, amino terminus; C, carboxyl terminus of the
Nit domain. Structure determination of NitFhit. (a) A portion
of the 2.8 Å experimental electron density map in stereo.
The map was contoured at 1.5 σ and superimposed on the refined
atomic model. (b) Stereo ribbon view of the Nit domain of a
NitFhit monomer (northern conformation). Secondary structural
elements are indicated. The Fhit domain, carboxy terminal to the
Nit domain, and three additional subunits of the NitFhit
tetramer are not shown. N, amino terminus; C, carboxyl terminus
of the Nit domain.
|
|
Figure 6.
A putative Nit active site. The region around Cys169, a residue
conserved in nitrilases, is conserved in Nit proteins. Residues
aligning with Cys169, Glu54 and Lys127 are predicted to form a
catalytic triad in the nitrilase superfamily. A putative Nit
active site. The region around Cys169, a residue conserved in
nitrilases, is conserved in Nit proteins. Residues aligning with
Cys169, Glu54 and Lys127 are predicted to form a catalytic triad
in the nitrilase superfamily.
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
with permission from Cell Press
|
|
|
|
|
|
|
