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PDBsum entry 1dmt

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protein ligands metals links
Hydrolase PDB id
1dmt
Jmol
Contents
Protein chain
696 a.a. *
Ligands
NAG ×3
RDF
GOL
Metals
_ZN
Waters ×465
* Residue conservation analysis
PDB id:
1dmt
Name: Hydrolase
Title: Structure of human neutral endopeptidase complexed with phos
Structure: Neutral endopeptidase. Chain: a. Fragment: extracellular domain. Synonym: neprilysin, nep, enkephalinase, common acute lymph leukemia antigen. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
2.10Å     R-factor:   0.195     R-free:   0.242
Authors: C.Oefner,A.D'Arcy,M.Hennig,F.K.Winkler,G.E.Dale
Key ref:
C.Oefner et al. (2000). Structure of human neutral endopeptidase (Neprilysin) complexed with phosphoramidon. J Mol Biol, 296, 341-349. PubMed id: 10669592 DOI: 10.1006/jmbi.1999.3492
Date:
15-Dec-99     Release date:   20-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08473  (NEP_HUMAN) -  Neprilysin
Seq:
Struc:
 
Seq:
Struc:
750 a.a.
696 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.24.11  - Neprilysin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage at the amino group of hydrophobic residues in insulin, casein, hemoglobin, and a number of other proteins and polypeptides.
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     neuron projection terminus   12 terms 
  Biological process     cellular response to cytokine stimulus   12 terms 
  Biochemical function     protein binding     9 terms  

 

 
DOI no: 10.1006/jmbi.1999.3492 J Mol Biol 296:341-349 (2000)
PubMed id: 10669592  
 
 
Structure of human neutral endopeptidase (Neprilysin) complexed with phosphoramidon.
C.Oefner, A.D'Arcy, M.Hennig, F.K.Winkler, G.E.Dale.
 
  ABSTRACT  
 
Neutral endopeptidase is a mammalian type II integral membrane zinc-containing endopeptidase, which degrades and inactivates a number of bioactive peptides. The range of substrates cleaved by neutral endopeptidase in vitro includes the enkephalins, substance P, endothelin, bradykinin and atrial natriuretic factor. Due to the physiological importance of neutral endopeptidase in the modulation of nociceptive and pressor responses there is considerable interest in inhibitors of this enzyme as novel analgesics and anti-hypertensive agents. Here we describe the crystal structure of the extracellular domain (residues 52-749) of human NEP complexed with the generic metalloproteinase inhibitor phosphoramidon at 2.1 A resolution. The structure reveals two multiply connected folding domains which embrace a large central cavity containing the active site. The inhibitor is bound to one side of this cavity and its binding mode provides a detailed understanding of the ligand-binding and specificity determinants.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Ribbon plot of sNEP depicting the volume of the active site cavity.
Figure 5.
Figure 5. Inhibitor binding to the active site of human sNEP. (a) Stereo view of the active site inhibited by phosphoramidon, green. Hydrogen bonds and ionic interactions are indicated by broken lines, a-helices are shown as cylinders, b-strands are represented by arrows: catalytic domain, violet; the smaller domain 2, blue; the three interdomain linker fragments, cyan. The zinc ion is shown in yellow. (b) Molecular surface of the phosphoramidon recognition site colored by electrostatic potential: positive, blue; negative, red.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 296, 341-349) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23275160 A.Ruf, M.Stihle, J.Benz, M.Schmidt, and H.Sobek (2013).
Structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa.
  Acta Crystallogr D Biol Crystallogr, 69, 24-31.
PDB codes: 4b52 4ger
21175663 N.M.Burton, and G.Daniels (2011).
Structural modelling of red cell surface proteins.
  Vox Sang, 100, 129-139.  
21425402 V.Maguer-Satta, R.Besançon, and E.Bachelard-Cascales (2011).
Concise review: neutral endopeptidase (CD10): a multifaceted environment actor in stem cells, physiological mechanisms, and cancer.
  Stem Cells, 29, 389-396.  
19585464 G.A.Dalkas, A.Papakyriakou, A.Vlamis-Gardikas, and G.A.Spyroulias (2009).
Insights into the anthrax lethal factor-substrate interaction and selectivity using docking and molecular dynamics simulations.
  Protein Sci, 18, 1774-1785.  
18470479 E.Malito, R.E.Hulse, and W.J.Tang (2008).
Amyloid beta-degrading cryptidases: insulin degrading enzyme, presequence peptidase, and neprilysin.
  Cell Mol Life Sci, 65, 2574-2585.  
18317569 G.D.Van Vickle, C.L.Esh, T.A.Kokjohn, R.L.Patton, W.M.Kalback, D.C.Luehrs, T.G.Beach, A.J.Newel, F.Lopera, B.Ghetti, R.Vidal, E.M.Castaño, and A.E.Roher (2008).
Presenilin-1 280Glu-->Ala mutation alters C-terminal APP processing yielding longer abeta peptides: implications for Alzheimer's disease.
  Mol Med, 14, 184-194.  
18507370 K.Gagnidze, Sachchidanand, R.Rozenfeld, M.Mezei, M.M.Zhou, and L.A.Devi (2008).
Homology modeling and site-directed mutagenesis to identify selective inhibitors of endothelin-converting enzyme-2.
  J Med Chem, 51, 3378-3387.  
18215274 N.D.Bland, J.W.Pinney, J.E.Thomas, A.J.Turner, and R.E.Isaac (2008).
Bioinformatic analysis of the neprilysin (M13) family of peptidases reveals complex evolutionary and functional relationships.
  BMC Evol Biol, 8, 16.  
18550518 P.K.Baral, N.Jajcanin-Jozić, S.Deller, P.Macheroux, M.Abramić, and K.Gruber (2008).
The first structure of dipeptidyl-peptidase III provides insight into the catalytic mechanism and mode of substrate binding.
  J Biol Chem, 283, 22316-22324.
PDB code: 3csk
18411275 R.E.Llovera, M.de Tullio, L.G.Alonso, M.A.Leissring, S.B.Kaufman, A.E.Roher, G.de Prat Gay, L.Morelli, and E.M.Castaño (2008).
The catalytic domain of insulin-degrading enzyme forms a denaturant-resistant complex with amyloid beta peptide: implications for Alzheimer disease pathogenesis.
  J Biol Chem, 283, 17039-17048.  
18597632 W.N.Addison, Y.Nakano, T.Loisel, P.Crine, and M.D.McKee (2008).
MEPE-ASARM peptides control extracellular matrix mineralization by binding to hydroxyapatite: an inhibition regulated by PHEX cleavage of ASARM.
  J Bone Miner Res, 23, 1638-1649.  
17429823 B.M.McArdle, and R.J.Quinn (2007).
Identification of protein fold topology shared between different folds inhibited by natural products.
  Chembiochem, 8, 788-798.  
17704566 C.Oefner, S.Pierau, H.Schulz, and G.E.Dale (2007).
Structural studies of a bifunctional inhibitor of neprilysin and DPP-IV.
  Acta Crystallogr D Biol Crystallogr, 63, 975-981.
PDB code: 2qpj
17251185 E.J.Lim, S.Sampath, J.Coll-Rodriguez, J.Schmidt, K.Ray, and D.W.Rodgers (2007).
Swapping the substrate specificities of the neuropeptidases neurolysin and thimet oligopeptidase.
  J Biol Chem, 282, 9722-9732.
PDB codes: 2o36 2o3e
17391066 N.M.Barros, M.Campos, P.A.Bersanetti, V.Oliveira, M.A.Juliano, G.Boileau, L.Juliano, and A.K.Carmona (2007).
Neprilysin carboxydipeptidase specificity studies and improvement in its detection with fluorescence energy transfer peptides.
  Biol Chem, 388, 447-455.  
17878751 P.Daull, A.Y.Jeng, and B.Battistini (2007).
Towards triple vasopeptidase inhibitors for the treatment of cardiovascular diseases.
  J Cardiovasc Pharmacol, 50, 247-256.  
16492151 G.N.Maw, A.Stobie, S.Planken, D.C.Pryde, V.Sanderson, M.Y.Platts, M.Corless, P.Stacey, C.Wayman, P.Van Der Graaf, C.Kohl, S.Coggon, and K.Beaumont (2006).
The discovery of small molecule inhibitors of neutral endopeptidase. Structure-activity studies on functionalized glutaramides.
  Chem Biol Drug Des, 67, 74-77.  
16934067 S.Lee, A.K.Debnath, X.Wu, T.Scofield, T.George, R.Kakaiya, M.G.Yogore, L.Sausais, M.Yacob, C.Lomas-Francis, and M.E.Reid (2006).
Molecular basis of two novel high-prevalence antigens in the Kell blood group system, KALT and KTIM.
  Transfusion, 46, 1323-1327.  
15769748 A.Clapéron, C.Rose, P.Gane, E.Collec, O.Bertrand, and T.Ouimet (2005).
The Kell protein of the common K2 phenotype is a catalytically active metalloprotease, whereas the rare Kell K1 antigen is inactive. Identification of novel substrates for the Kell protein.
  J Biol Chem, 280, 21272-21283.  
16112736 N.Iwata, M.Higuchi, and T.C.Saido (2005).
Metabolism of amyloid-beta peptide and Alzheimer's disease.
  Pharmacol Ther, 108, 129-148.  
14747736 C.Oefner, B.P.Roques, M.C.Fournie-Zaluski, and G.E.Dale (2004).
Structural analysis of neprilysin with various specific and potent inhibitors.
  Acta Crystallogr D Biol Crystallogr, 60, 392-396.
PDB codes: 1r1h 1r1i 1r1j
15009531 N.Inguimbert, H.Poras, H.Dhotel, F.Beslot, E.Scalbert, C.Bennejean, P.Renard, M.C.Fournié-Zaluski, and B.P.Roques (2004).
In vivo properties of thiol inhibitors of the three vasopeptidases NEP, ACE and ECE are improved by introduction of a 7-azatryptophan in P2' position.
  J Pept Res, 63, 99.  
15239059 S.Sahli, B.Stump, T.Welti, D.Blum-Kaelin, J.D.Aebi, C.Oefner, H.J.Böhm, and F.Diederich (2004).
Structure-based design, synthesis, and in vitro evaluation of nonpeptidic neprilysin inhibitors.
  Chembiochem, 5, 996.  
15294904 S.Voisin, D.Rognan, C.Gros, and T.Ouimet (2004).
A three-dimensional model of the neprilysin 2 active site based on the X-ray structure of neprilysin. Identification of residues involved in substrate hydrolysis and inhibitor binding of neprilysin 2.
  J Biol Chem, 279, 46172-46181.  
12832764 C.Oefner, A.D'Arcy, A.Mac Sweeney, S.Pierau, R.Gardiner, and G.E.Dale (2003).
High-resolution structure of human apo dipeptidyl peptidase IV/CD26 and its complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrolidine.
  Acta Crystallogr D Biol Crystallogr, 59, 1206-1212.
PDB code: 1pfq
12835417 C.Rougeot, M.Messaoudi, V.Hermitte, A.G.Rigault, T.Blisnick, C.Dugave, D.Desor, and F.Rougeon (2003).
Sialorphin, a natural inhibitor of rat membrane-bound neutral endopeptidase that displays analgesic activity.
  Proc Natl Acad Sci U S A, 100, 8549-8554.  
12832763 M.Selkti, A.Tomas, J.F.Gaucher, T.Prangé, M.C.Fournié-Zaluski, H.Chen, and B.P.Roques (2003).
Interactions of a new alpha-aminophosphinic derivative inside the active site of TLN (thermolysin): a model for zinc-metalloendopeptidase inhibition.
  Acta Crystallogr D Biol Crystallogr, 59, 1200-1205.
PDB codes: 1no0 1os0
12605218 N.M.Hooper, and A.J.Turner (2003).
An ACE structure.
  Nat Struct Biol, 10, 155-157.  
12874285 S.Liu, R.Guo, L.G.Simpson, Z.S.Xiao, C.E.Burnham, and L.D.Quarles (2003).
Regulation of fibroblastic growth factor 23 expression but not degradation by PHEX.
  J Biol Chem, 278, 37419-37426.  
12801742 S.Tsubuki, Y.Takaki, and T.C.Saido (2003).
Dutch, Flemish, Italian, and Arctic mutations of APP and resistance of Abeta to physiologically relevant proteolytic degradation.
  Lancet, 361, 1957-1958.  
12067222 J.A.Carson, and A.J.Turner (2002).
Beta-amyloid catabolism: roles for neprilysin (NEP) and other metallopeptidases?
  J Neurochem, 81, 1-8.  
12001226 L.Bianchetti, C.Oudet, and O.Poch (2002).
M13 endopeptidases: New conserved motifs correlated with structure, and simultaneous phylogenetic occurrence of PHEX and the bony fish.
  Proteins, 47, 481-488.  
12042323 R.Rozenfeld, X.Iturrioz, B.Maigret, and C.Llorens-Cortes (2002).
Contribution of molecular modeling and site-directed mutagenesis to the identification of two structural residues, Arg-220 and Asp-227, in aminopeptidase A.
  J Biol Chem, 277, 29242-29252.  
11223883 A.J.Turner, R.E.Isaac, and D.Coates (2001).
The neprilysin (NEP) family of zinc metalloendopeptidases: genomics and function.
  Bioessays, 23, 261-269.  
11277498 B.P.Roques (2001).
Insights into peptide and protein function: a convergent approach.
  J Pept Sci, 7, 63-73.  
11248043 C.K.Brown, K.Madauss, W.Lian, M.R.Beck, W.D.Tolbert, and D.W.Rodgers (2001).
Structure of neurolysin reveals a deep channel that limits substrate access.
  Proc Natl Acad Sci U S A, 98, 3127-3132.
PDB code: 1i1i
11558680 I.Kishimoto, F.K.Hamra, and D.L.Garbers (2001).
Apparent B-type natriuretic peptide selectivity in the kidney due to differential processing.
  Can J Physiol Pharmacol, 79, 715-722.  
11560781 N.Bonvouloir, N.Lemieux, P.Crine, G.Boileau, and L.DesGroseillers (2001).
Molecular cloning, tissue distribution, and chromosomal localization of MMEL2, a gene coding for a novel human member of the neutral endopeptidase-24.11 family.
  DNA Cell Biol, 20, 493-498.  
11264666 Y.Sekine-Aizawa, E.Hama, K.Watanabe, S.Tsubuki, M.Kanai-Azuma, Y.Kanai, H.Arai, H.Aizawa, N.Iwata, and T.C.Saido (2001).
Matrix metalloproteinase (MMP) system in brain: identification and characterization of brain-specific MMP highly expressed in cerebellum.
  Eur J Neurosci, 13, 935-948.  
11092934 W.Lian, G.Chen, D.Wu, C.K.Brown, K.Madauss, L.B.Hersh, and D.W.Rodgers (2000).
Crystallization and preliminary analysis of neurolysin.
  Acta Crystallogr D Biol Crystallogr, 56, 1644-1646.  
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.