PDBsum entry 1igb

Aminopeptidase

PDB id

1igb

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Contents

			Protein chain

					291 a.a. *

			Ligands

					IPO

			Metals

					_ZN ×2

			Waters ×660

* Residue conservation analysis

PDB id:

1igb

Links

Name:

Aminopeptidase

Title:

Aeromonas proteolytica aminopeptidase complexed with the inhibitor para-iodo-d-phenylalanine hydroxamate

Structure:

Aminopeptidase. Chain: a. Ec: 3.4.11.10

Source:

Vibrio proteolyticus. Organism_taxid: 671

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å

R-factor:

0.160

R-free:

0.241

Authors:

B.Chevrier,H.D'Orchymont,C.Schalk,C.Tarnus,D.Moras

Key ref:

B.Chevrier et al. (1996). The structure of the Aeromonas proteolytica aminopeptidase complexed with a hydroxamate inhibitor. Involvement in catalysis of Glu151 and two zinc ions of the co-catalytic unit. Eur J Biochem, 237, 393-398. PubMed id: 8647077

Date:

27-Feb-96

Release date:

01-Aug-96

PROCHECK

	Headers

	References

Protein chain

Q01693 (AMPX_VIBPR) - Bacterial leucyl aminopeptidase from Vibrio proteolyticus

Seq: Struc:					504 a.a. 291 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.4.11.10 - bacterial leucyl aminopeptidase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids.

Cofactor:

Zn(2+)

	Eur J Biochem 237:393-398 (1996)
PubMed id: 8647077

The structure of the Aeromonas proteolytica aminopeptidase complexed with a hydroxamate inhibitor. Involvement in catalysis of Glu151 and two zinc ions of the co-catalytic unit.
B.Chevrier, H.D'Orchymont, C.Schalk, C.Tarnus, D.Moras.

ABSTRACT

The structure of the complex of Aeromonas proteolytica aminopeptidase, a two-zinc exopeptidase, with the inhibitor p-iodo-D-phenylalanine hydroxamate has been determined by X-ray crystallography. Refinement of the structure, which includes 220 water molecules, using data at 0.80-0.23-nm resolution resulted in a crystallographic residual R value of 16%. The hydroxamate group adopts a planar conformation whereby the two oxygen atoms interact with the zinc ions. The N-hydroxyl group of the inhibitor is located between the two zinc ions, a position which is close to that occupied by a water molecule in the native structure. The carbonyl oxygen of the inhibitor binds to Zn1, which becomes pentacoordinated while Zn2 remains tetracoordinated, in contrast to the native protein where both zinc ions were shown to be tetracoordinated and structurally equivalent. Interactions of the carboxylate oxygens of Glu151 with the hydroxamate group play an important role in the stabilization of the complex.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20138056

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.

J Mol Biol, 397, 617-626.

PDB codes:

3ic1 3isz

20610394

T.S.Girish, and B.Gopal (2010).
Crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese-bound and apo-states.

J Biol Chem, 285, 29406-29415.

PDB codes:

3khx 3khz 3ki9

17608735

Y.F.Hershcovitz, R.Gilboa, V.Reiland, G.Shoham, and Y.Shoham (2007).
Catalytic mechanism of SGAP, a double-zinc aminopeptidase from Streptomyces griseus.

FEBS J, 274, 3864-3876.

16780565

C.Argueta, K.Yuksek, R.Patel, and M.L.Summers (2006).
Identification of Nostoc punctiforme akinete-expressed genes using differential display.

Mol Microbiol, 61, 748-757.

17028223

J.Arima, Y.Uesugi, M.Iwabuchi, and T.Hatanaka (2006).
Change in substrate preference of Streptomyces aminopeptidase through modification of the environment around the substrate binding site.

Appl Environ Microbiol, 72, 7962-7967.

16421726

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.

J Biol Inorg Chem, 11, 206-216.

16244434

K.Mori, and K.Ishikawa (2005).
New deblocking aminopeptidases from Pyrococcus horikoshii.

Biosci Biotechnol Biochem, 69, 1854-1860.

15837926

M.I.Davis, M.J.Bennett, L.M.Thomas, and P.J.Bjorkman (2005).
Crystal structure of prostate-specific membrane antigen, a tumor marker and peptidase.

Proc Natl Acad Sci U S A, 102, 5981-5986.

PDB code:

1z8l

15668014

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.

FEMS Microbiol Lett, 243, 157-163.

15138277

K.P.Bzymek, and R.C.Holz (2004).
The catalytic role of glutamate 151 in the leucine aminopeptidase from Aeromonas proteolytica.

J Biol Chem, 279, 31018-31025.

15375159

S.Russo, and U.Baumann (2004).
Crystal structure of a dodecameric tetrahedral-shaped aminopeptidase.

J Biol Chem, 279, 51275-51281.

PDB code:

1xfo

15583392

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.

Acta Crystallogr D Biol Crystallogr, 60, 2371-2376.

12524301

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.

Biophys J, 84, 489-500.

12632471

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.

J Comput Chem, 24, 565-581.

14583590

N.Schülke, O.A.Varlamova, G.P.Donovan, D.Ma, J.P.Gardner, D.M.Morrissey, R.R.Arrigale, C.Zhan, A.J.Chodera, K.G.Surowitz, P.J.Maddon, W.D.Heston, and W.C.Olson (2003).
The homodimer of prostate-specific membrane antigen is a functional target for cancer therapy.

Proc Natl Acad Sci U S A, 100, 12590-12595.

12405829

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.

J Am Chem Soc, 124, 13025-13034.

11940603

D.R.Hall, C.S.Bond, G.A.Leonard, C.I.Watt, A.Berry, and W.N.Hunter (2002).
Structure of tagatose-1,6-bisphosphate aldolase. Insight into chiral discrimination, mechanism, and specificity of class II aldolases.

J Biol Chem, 277, 22018-22024.

PDB code:

1gvf

11856302

K.Håkansson, and C.G.Miller (2002).
Structure of peptidase T from Salmonella typhimurium.

Eur J Biochem, 269, 443-450.

PDB code:

1fno

11484227

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.

PDB codes:

1f2o 1f2p

10684608

F.Javid-Majd, and J.S.Blanchard (2000).
Mechanistic analysis of the argE-encoded N-acetylornithine deacetylase.

Biochemistry, 39, 1285-1293.

10771423

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.

Acta Crystallogr D Biol Crystallogr, 56, 551-558.

PDB codes:

1cp7 1qq9

10413478

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.

Biochemistry, 38, 9048-9053.

PDB code:

1cp6

10531064

C.M.Lawrence, S.Ray, M.Babyonyshev, R.Galluser, D.W.Borhani, and S.C.Harrison (1999).
Crystal structure of the ectodomain of human transferrin receptor.

Science, 286, 779-782.

PDB code:

1cx8

10595564

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.

10569943

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.

10085079

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.

10206990

R.Gingras, C.Richard, M.El-Alfy, C.R.Morales, M.Potier, and A.V.Pshezhetsky (1999).
Purification, cDNA cloning, and expression of a new human blood plasma glutamate carboxypeptidase homologous to N-acetyl-aspartyl-alpha-glutamate carboxypeptidase/prostate-specific membrane antigen.

J Biol Chem, 274, 11742-11750.

10387007

W.T.Lowther, A.M.Orville, D.T.Madden, S.Lim, D.H.Rich, and B.W.Matthews (1999).
Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis.

Biochemistry, 38, 7678-7688.

PDB codes:

2mat 3mat 4mat

9685395

C.H.Halsted, E.H.Ling, R.Luthi-Carter, J.A.Villanueva, J.M.Gardner, and J.T.Coyle (1998).
Folylpoly-gamma-glutamate carboxypeptidase from pig jejunum. Molecular characterization and relation to glutamate carboxypeptidase II.

J Biol Chem, 273, 20417-20424.

9667939

J.E.Coleman (1998).
Zinc enzymes.

Curr Opin Chem Biol, 2, 222-234.

9671518

T.L.Born, R.Zheng, and J.S.Blanchard (1998).
Hydrolysis of N-succinyl-L,L-diaminopimelic acid by the Haemophilus influenzae dapE-encoded desuccinylase: metal activation, solvent isotope effects, and kinetic mechanism.

Biochemistry, 37, 10478-10487.

9108146

A.F.Neuwald, J.S.Liu, D.J.Lipman, and C.E.Lawrence (1997).
Extracting protein alignment models from the sequence database.

Nucleic Acids Res, 25, 1665-1677.

9245416

B.Bennett, and R.C.Holz (1997).
Spectroscopically distinct cobalt(II) sites in heterodimetallic forms of the aminopeptidase from Aeromonas proteolytica: characterization of substrate binding.

Biochemistry, 36, 9837-9846.

9100023

G.Chen, T.Edwards, V.M.D'souza, and R.C.Holz (1997).
Mechanistic studies on the aminopeptidase from Aeromonas proteolytica: a two-metal ion mechanism for peptide hydrolysis.

Biochemistry, 36, 4278-4286.

9083113

S.Rowsell, R.A.Pauptit, A.D.Tucker, R.G.Melton, D.M.Blow, and P.Brick (1997).
Crystal structure of carboxypeptidase G2, a bacterial enzyme with applications in cancer therapy.

Structure, 5, 337-347.

PDB code:

1cg2

8939754

S.J.Cooper, G.A.Leonard, S.M.McSweeney, A.W.Thompson, J.H.Naismith, S.Qamar, A.Plater, A.Berry, and W.N.Hunter (1996).
The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold.

Structure, 4, 1303-1315.

PDB code:

1zen

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.