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PDBsum entry 1amp
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Hydrolase(aminopeptidase)
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PDB id
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1amp
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* Residue conservation analysis
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Enzyme class:
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E.C.3.4.11.10
- bacterial leucyl aminopeptidase.
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Reaction:
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Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids.
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Cofactor:
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Zn(2+)
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DOI no:
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Structure
2:283-291
(1994)
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PubMed id:
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Crystal structure of Aeromonas proteolytica aminopeptidase: a prototypical member of the co-catalytic zinc enzyme family.
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B.Chevrier,
C.Schalk,
H.D'Orchymont,
J.M.Rondeau,
D.Moras,
C.Tarnus.
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ABSTRACT
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BACKGROUND: Aminopeptidases specifically cleave the amino-terminal residue from
polypeptide chains and are involved in the metabolism of biologically active
peptides. The family includes zinc-dependent enzymes possessing either one or
two zinc ions per active site. Structural studies providing a detailed view of
the metal environment may reveal whether the one-zinc and two-zinc enzymes
constitute structurally and mechanistically distinct subclasses, and what role
the metal ions play in the catalytic process. RESULTS: We have solved the
crystal structure of the monomeric aminopeptidase from Aeromonas proteolytica at
1.8 A resolution. The protein is folded into a single alpha/beta globular
domain. The active site contains two zinc ions (3.5 A apart) with shared ligands
and symmetrical coordination spheres. We have compared it with the related
bovine lens leucine aminopeptidase and the cobalt-containing Escherichia coli
methionine aminopeptidase. CONCLUSIONS: The environment and coordination of the
two zinc ions in A. proteolytica aminopeptidase strongly support the view that
the two metal ions constitute a co-catalytic unit and play equivalent roles
during catalysis. This conflicts with the conclusions drawn from the related
bovine leucine aminopeptidase and early biochemical studies. In addition, the
known specificity of the aminopeptidase for hydrophobic amino-terminal residues
is reflected in the hydrophobicity of the active site cleft.
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Selected figure(s)
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Figure 3.
Figure 3. (a) Stereoview of the zinc ligands in the
metal-binding site. Dashed lines indicate the strong
zinc–ligand interactions. (b) Stereoview of the electron
density contoured at 1.5 σ level. This view emphasizes the
bidendate character of the Zn2– carboxylate interaction with
Asp179. A similar interaction is observed between Glu152 (not
labeled) and Zn1. Figure 3. (a) Stereoview of the zinc
ligands in the metal-binding site. Dashed lines indicate the
strong zinc–ligand interactions. (b) Stereoview of the
electron density contoured at 1.5 σ level. This view emphasizes
the bidendate character of the Zn2– carboxylate interaction
with Asp179. A similar interaction is observed between Glu152
(not labeled) and Zn1.
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Figure 7.
Figure 7. Histogram plotting the number of water molecules with
respect to their distance from the closest polar protein atoms.
Figure 7. Histogram plotting the number of water molecules
with respect to their distance from the closest polar protein
atoms.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(1994,
2,
283-291)
copyright 1994.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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B.P.Nocek,
D.M.Gillner,
Y.Fan,
R.C.Holz,
and
A.Joachimiak
(2010).
Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.
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J Mol Biol,
397,
617-626.
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PDB codes:
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C.Y.Chang,
Y.C.Hsieh,
T.Y.Wang,
C.J.Chen,
and
T.K.Wu
(2009).
Purification, crystallization and preliminary X-ray analysis of an aminoacylhistidine dipeptidase (PepD) from Vibrio alginolyticus.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
216-218.
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D.M.Gillner,
D.L.Bienvenue,
B.P.Nocek,
A.Joachimiak,
V.Zachary,
B.Bennett,
and
R.C.Holz
(2009).
The dapE-encoded N-succinyl-L: ,L: -diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues.
|
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J Biol Inorg Chem,
14,
1.
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M.A.Durá,
E.Rosenbaum,
A.Larabi,
F.Gabel,
F.M.Vellieux,
and
B.Franzetti
(2009).
The structural and biochemical characterizations of a novel TET peptidase complex from Pyrococcus horikoshii reveal an integrated peptide degradation system in hyperthermophilic Archaea.
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Mol Microbiol,
72,
26-40.
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PDB codes:
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M.Y.Zakharova,
N.A.Kuznetsov,
S.A.Dubiley,
A.V.Kozyr,
O.S.Fedorova,
D.M.Chudakov,
D.G.Knorre,
I.G.Shemyakin,
A.G.Gabibov,
and
A.V.Kolesnikov
(2009).
Substrate Recognition of Anthrax Lethal Factor Examined by Combinatorial and Pre-steady-state Kinetic Approaches.
|
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J Biol Chem,
284,
17902-17913.
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A.B.Curtiss,
M.Bera,
G.T.Musie,
and
D.R.Powell
(2008).
Synthesis and characterization of mono- and micro6-sulfato hexanuclear zinc complexes of a new symmetric dinucleating ligand.
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Dalton Trans,
(),
2717-2724.
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H.Unno,
T.Yamashita,
S.Ujita,
N.Okumura,
H.Otani,
A.Okumura,
K.Nagai,
and
M.Kusunoki
(2008).
Structural Basis for Substrate Recognition and Hydrolysis by Mouse Carnosinase CN2.
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J Biol Chem,
283,
27289-27299.
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PDB codes:
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O.Rossier,
J.Dao,
and
N.P.Cianciotto
(2008).
The type II secretion system of Legionella pneumophila elaborates two aminopeptidases, as well as a metalloprotease that contributes to differential infection among protozoan hosts.
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Appl Environ Microbiol,
74,
753-761.
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B.Geueke,
and
H.P.Kohler
(2007).
Bacterial beta-peptidyl aminopeptidases: on the hydrolytic degradation of beta-peptides.
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Appl Microbiol Biotechnol,
74,
1197-1204.
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J.R.Hershfield,
N.Pattabiraman,
C.N.Madhavarao,
and
M.A.Namboodiri
(2007).
Mutational analysis of aspartoacylase: implications for Canavan disease.
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Brain Res,
1148,
1.
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W.C.McGregor,
S.I.Swierczek,
B.Bennett,
and
R.C.Holz
(2007).
Characterization of the catalytically active Mn(II)-loaded argE-encoded N-acetyl-L-ornithine deacetylase from Escherichia coli.
|
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J Biol Inorg Chem,
12,
603-613.
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Y.F.Hershcovitz,
R.Gilboa,
V.Reiland,
G.Shoham,
and
Y.Shoham
(2007).
Catalytic mechanism of SGAP, a double-zinc aminopeptidase from Streptomyces griseus.
|
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FEBS J,
274,
3864-3876.
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G.Schoehn,
F.M.Vellieux,
M.Asunción Durá,
V.Receveur-Bréchot,
C.M.Fabry,
R.W.Ruigrok,
C.Ebel,
A.Roussel,
and
B.Franzetti
(2006).
An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron.
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J Biol Chem,
281,
36327-36337.
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PDB code:
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H.E.Stimpson,
M.J.Lewis,
and
H.R.Pelham
(2006).
Transferrin receptor-like proteins control the degradation of a yeast metal transporter.
|
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EMBO J,
25,
662-672.
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J.Arima,
Y.Uesugi,
M.Iwabuchi,
and
T.Hatanaka
(2006).
Study on peptide hydrolysis by aminopeptidases from Streptomyces griseus, Streptomyces septatus and Aeromonas proteolytica.
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Appl Microbiol Biotechnol,
70,
541-547.
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J.Arima,
Y.Uesugi,
M.Uraji,
M.Iwabuchi,
and
T.Hatanaka
(2006).
Dipeptide synthesis by an aminopeptidase from Streptomyces septatus TH-2 and its application to synthesis of biologically active peptides.
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Appl Environ Microbiol,
72,
4225-4231.
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J.Arima,
Y.Uesugi,
M.Uraji,
S.Yatsushiro,
S.Tsuboi,
M.Iwabuchi,
and
T.Hatanaka
(2006).
Modulation of Streptomyces leucine aminopeptidase by calcium: identification and functional analysis of key residues in activation and stabilization by calcium.
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J Biol Chem,
281,
5885-5894.
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J.R.Mesters,
C.Barinka,
W.Li,
T.Tsukamoto,
P.Majer,
B.S.Slusher,
J.Konvalinka,
and
R.Hilgenfeld
(2006).
Structure of glutamate carboxypeptidase II, a drug target in neuronal damage and prostate cancer.
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EMBO J,
25,
1375-1384.
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PDB codes:
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R.Davis,
D.Bienvenue,
S.I.Swierczek,
D.M.Gilner,
L.Rajagopal,
B.Bennett,
and
R.C.Holz
(2006).
Kinetic and spectroscopic characterization of the E134A- and E134D-altered dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae.
|
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J Biol Inorg Chem,
11,
206-216.
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W.Desmarais,
D.L.Bienvenue,
K.P.Bzymek,
G.A.Petsko,
D.Ringe,
and
R.C.Holz
(2006).
The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica.
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J Biol Inorg Chem,
11,
398-408.
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PDB codes:
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G.Y.Hwang,
L.Y.Kuo,
M.R.Tsai,
S.L.Yang,
and
L.L.Lin
(2005).
Histidines 345 and 378 of Bacillus stearothermophilus leucine aminopeptidase II are essential for the catalytic activity of the enzyme.
|
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Antonie Van Leeuwenhoek,
87,
355-359.
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G.Yang,
R.Miao,
Y.Li,
J.Hong,
C.Zhao,
Z.Guo,
and
L.Zhu
(2005).
Synergic effect of two metal centers in catalytic hydrolysis of methionine-containing peptides promoted by dinuclear palladium(II) hexaazacyclooctadecane complex.
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Dalton Trans,
(),
1613-1619.
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K.F.Huang,
Y.L.Liu,
W.J.Cheng,
T.P.Ko,
and
A.H.Wang
(2005).
Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation.
|
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Proc Natl Acad Sci U S A,
102,
13117-13122.
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PDB codes:
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Y.Fundoiano-Hershcovitz,
L.Rabinovitch,
S.Shulami,
V.Reiland,
G.Shoham,
and
Y.Shoham
(2005).
The ywad gene from Bacillus subtilis encodes a double-zinc aminopeptidase.
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FEMS Microbiol Lett,
243,
157-163.
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C.Barinka,
P.Mlcochová,
P.Sácha,
I.Hilgert,
P.Majer,
B.S.Slusher,
V.Horejsí,
and
J.Konvalinka
(2004).
Amino acids at the N- and C-termini of human glutamate carboxypeptidase II are required for enzymatic activity and proper folding.
|
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Eur J Biochem,
271,
2782-2790.
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C.Barinka,
P.Sácha,
J.Sklenár,
P.Man,
K.Bezouska,
B.S.Slusher,
and
J.Konvalinka
(2004).
Identification of the N-glycosylation sites on glutamate carboxypeptidase II necessary for proteolytic activity.
|
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Protein Sci,
13,
1627-1635.
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K.P.Bzymek,
and
R.C.Holz
(2004).
The catalytic role of glutamate 151 in the leucine aminopeptidase from Aeromonas proteolytica.
|
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J Biol Chem,
279,
31018-31025.
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M.Ribó,
M.Bosch,
G.Torrent,
A.Benito,
B.Beaumelle,
and
M.Vilanova
(2004).
Quantitative analysis, using MALDI-TOF mass spectrometry, of the N-terminal hydrolysis and cyclization reactions of the activation process of onconase.
|
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Eur J Biochem,
271,
1163-1171.
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R.E.Booth,
S.C.Lovell,
S.A.Misquitta,
and
R.C.Bateman
(2004).
Human glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site.
|
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BMC Biol,
2,
2.
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S.Russo,
and
U.Baumann
(2004).
Crystal structure of a dodecameric tetrahedral-shaped aminopeptidase.
|
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J Biol Chem,
279,
51275-51281.
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PDB code:
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V.Reiland,
R.Gilboa,
A.Spungin-Bialik,
D.Schomburg,
Y.Shoham,
S.Blumberg,
and
G.Shoham
(2004).
Binding of inhibitory aromatic amino acids to Streptomyces griseus aminopeptidase.
|
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Acta Crystallogr D Biol Crystallogr,
60,
1738-1746.
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PDB codes:
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V.Reiland,
Y.Fundoiano-Hershcovitz,
G.Golan,
R.Gilboa,
Y.Shoham,
and
G.Shoham
(2004).
Preliminary crystallographic characterization of BSAP, an extracellular aminopeptidase from Bacillus subtilis.
|
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Acta Crystallogr D Biol Crystallogr,
60,
2371-2376.
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C.J.Ackerman,
M.M.Harnett,
W.Harnett,
S.M.Kelly,
D.I.Svergun,
and
O.Byron
(2003).
19 A solution structure of the filarial nematode immunomodulatory protein, ES-62.
|
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Biophys J,
84,
489-500.
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H.A.Lindner,
V.V.Lunin,
A.Alary,
R.Hecker,
M.Cygler,
and
R.Ménard
(2003).
Essential roles of zinc ligation and enzyme dimerization for catalysis in the aminoacylase-1/M20 family.
|
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J Biol Chem,
278,
44496-44504.
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PDB code:
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M.Elstner,
Q.Cui,
P.Munih,
E.Kaxiras,
T.Frauenheim,
and
M.Karplus
(2003).
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis.
|
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J Comput Chem,
24,
565-581.
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B.Bennett,
W.E.Antholine,
V.M.D'souza,
G.Chen,
L.Ustinyuk,
and
R.C.Holz
(2002).
Structurally distinct active sites in the copper(II)-substituted aminopeptidases from Aeromonas proteolytica and Escherichia coli.
|
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J Am Chem Soc,
124,
13025-13034.
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K.Håkansson,
and
C.G.Miller
(2002).
Structure of peptidase T from Salmonella typhimurium.
|
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Eur J Biochem,
269,
443-450.
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PDB code:
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R.Cahan,
I.Axelrad,
M.Safrin,
D.E.Ohman,
and
E.Kessler
(2001).
A secreted aminopeptidase of Pseudomonas aeruginosa. Identification, primary structure, and relationship to other aminopeptidases.
|
| |
J Biol Chem,
276,
43645-43652.
|
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R.Gilboa,
A.Spungin-Bialik,
G.Wohlfahrt,
D.Schomburg,
S.Blumberg,
and
G.Shoham
(2001).
Interactions of Streptomyces griseus aminopeptidase with amino acid reaction products and their implications toward a catalytic mechanism.
|
| |
Proteins,
44,
490-504.
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PDB codes:
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C.Bompard-Gilles,
V.Villeret,
G.J.Davies,
L.Fanuel,
B.Joris,
J.M.Frère,
and
J.Van Beeumen
(2000).
A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi.
|
| |
Structure,
8,
153-162.
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PDB code:
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M.Abramić,
D.Schleuder,
L.Dolovcak,
W.Schröder,
K.Strupat,
D.Sagi,
J.Peter-Katalini,
and
L.Vitale
(2000).
Human and rat dipeptidyl peptidase III: biochemical and mass spectrometric arguments for similarities and differences.
|
| |
Biol Chem,
381,
1233-1243.
|
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R.Gilboa,
H.M.Greenblatt,
M.Perach,
A.Spungin-Bialik,
U.Lessel,
G.Wohlfahrt,
D.Schomburg,
S.Blumberg,
and
G.Shoham
(2000).
Interactions of Streptomyces griseus aminopeptidase with a methionine product analogue: a structural study at 1.53 A resolution.
|
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Acta Crystallogr D Biol Crystallogr,
56,
551-558.
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PDB codes:
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C.C.De Paola,
B.Bennett,
R.C.Holz,
D.Ringe,
and
G.A.Petsko
(1999).
1-Butaneboronic acid binding to Aeromonas proteolytica aminopeptidase: a case of arrested development.
|
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Biochemistry,
38,
9048-9053.
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PDB code:
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D.Mahadevan,
and
J.W.Saldanha
(1999).
The extracellular regions of PSMA and the transferrin receptor contain an aminopeptidase domain: implications for drug design.
|
| |
Protein Sci,
8,
2546-2549.
|
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F.X.Gomis-Rüth,
V.Companys,
Y.Qian,
L.D.Fricker,
J.Vendrell,
F.X.Avilés,
and
M.Coll
(1999).
Crystal structure of avian carboxypeptidase D domain II: a prototype for the regulatory metallocarboxypeptidase subfamily.
|
| |
EMBO J,
18,
5817-5826.
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PDB code:
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K.M.Huntington,
D.L.Bienvenue,
Y.Wei,
B.Bennett,
R.C.Holz,
and
D.Pei
(1999).
Slow-binding inhibition of the aminopeptidase from Aeromonas proteolytica by peptide thiols: synthesis and spectroscopic characterization.
|
| |
Biochemistry,
38,
15587-15596.
|
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M.N.Pangalos,
J.M.Neefs,
M.Somers,
P.Verhasselt,
M.Bekkers,
L.van der Helm,
E.Fraiponts,
D.Ashton,
and
R.D.Gordon
(1999).
Isolation and expression of novel human glutamate carboxypeptidases with N-acetylated alpha-linked acidic dipeptidase and dipeptidyl peptidase IV activity.
|
| |
J Biol Chem,
274,
8470-8483.
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|
R.Gingras,
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PDB codes:
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A.G.Murzin
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How far divergent evolution goes in proteins.
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PDB code:
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Crystal structure of the zinc-dependent beta-lactamase from Bacillus cereus at 1.9 A resolution: binuclear active site with features of a mononuclear enzyme.
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Biochemistry,
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PDB code:
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Biochemistry,
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Spectroscopically distinct cobalt(II) sites in heterodimetallic forms of the aminopeptidase from Aeromonas proteolytica: characterization of substrate binding.
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PDB code:
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PDB code:
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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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