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PDBsum entry 1ew2

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protein ligands metals links
Hydrolase PDB id
1ew2
Jmol PyMol
Contents
Protein chain
479 a.a. *
Ligands
NAG
PO4
Metals
_ZN ×2
_MG ×2
Waters ×602
* Residue conservation analysis
PDB id:
1ew2
Name: Hydrolase
Title: Crystal structure of a human phosphatase
Structure: Phosphatase. Chain: a. Ec: 3.1.3.1
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: placenta
Biol. unit: Dimer (from PDB file)
Resolution:
1.82Å     R-factor:   0.185     R-free:   0.242
Authors: M.H.Le Du,T.Stigbrand,M.J.Taussig,A.Menez,E.A.Stura
Key ref:
M.H.Le Du et al. (2001). Crystal structure of alkaline phosphatase from human placenta at 1.8 A resolution. Implication for a substrate specificity. J Biol Chem, 276, 9158-9165. PubMed id: 11124260 DOI: 10.1074/jbc.M009250200
Date:
21-Apr-00     Release date:   04-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05187  (PPB1_HUMAN) -  Alkaline phosphatase, placental type
Seq:
Struc:
 
Seq:
Struc:
535 a.a.
479 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.1  - Alkaline phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphate monoester + H2O = an alcohol + phosphate
phosphate monoester
+ H(2)O
= alcohol
+
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
      Cofactor: Mg(2+); Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell surface   5 terms 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M009250200 J Biol Chem 276:9158-9165 (2001)
PubMed id: 11124260  
 
 
Crystal structure of alkaline phosphatase from human placenta at 1.8 A resolution. Implication for a substrate specificity.
M.H.Le Du, T.Stigbrand, M.J.Taussig, A.Menez, E.A.Stura.
 
  ABSTRACT  
 
Human placental alkaline phosphatase (PLAP) is one of three tissue-specific human APs extensively studied because of its ectopic expression in tumors. The crystal structure, determined at 1.8-A resolution, reveals that during evolution, only the overall features of the enzyme have been conserved with respect to Escherichia coli. The surface is deeply mutated with 8% residues in common, and in the active site, only residues strictly necessary to perform the catalysis have been preserved. Additional structural elements aid an understanding of the allosteric property that is specific for the mammalian enzyme (Hoylaerts, M. F., Manes, T., and Millán, J. L. (1997) J. Biol. Chem. 272, 22781-22787). Allostery is probably favored by the quality of the dimer interface, by a long N-terminal alpha-helix from one monomer that embraces the other one, and similarly by the exchange of a residue from one monomer in the active site of the other. In the neighborhood of the catalytic serine, the orientation of Glu-429, a residue unique to PLAP, and the presence of a hydrophobic pocket close to the phosphate product, account for the specific uncompetitive inhibition of PLAP by l-amino acids, consistent with the acquisition of substrate specificity. The location of the active site at the bottom of a large valley flanked by an interfacial crown-shaped domain and a domain containing an extra metal ion on the other side suggest that the substrate of PLAP could be a specific phosphorylated protein.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Electron density for carbohydrates and fourth metal ion. a and b, glycosylation site connected to Asn-122 corresponding, respectively, to the reported 1.8-Å structure (a) and to a 2.1-Å data set still under refinement (b) (Table I). c, carbohydrate connected to Asn-249 in stacking with Trp-248 and coordination of the fourth metal ion with Glu-216, Phe-269-CO, Glu-270-O 2, Asp-285, and one water molecule. In each case, the 2 F[o] F[c] map is shown in blue and is contoured at the 1.2 level. The F[o] F[c] map is shown in green and contoured at 10 level. This figure was made with TURBO (34).
Figure 5.
Fig. 5. Uncompetitive inhibition. Shown is modeling of L-Phe uncompetitive inhibitor in the active site of PLAP. The L-Phe amino acid is in stick representation colored in yellow. PLAP is in Corey-Pauling-Koltun representation with one monomer colored in white and the second colored in pink. Residues of PLAP interacting with L-Phe are colored in residue type: acidic in red, basic in blue, neutral in green, aromatic in violet. The metal ions are colored in orange. This figure was made with TURBO.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 9158-9165) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22902367 O.J.Harrison, J.Vendome, J.Brasch, X.Jin, S.Hong, P.S.Katsamba, G.Ahlsen, R.B.Troyanovsky, S.M.Troyanovsky, B.Honig, and L.Shapiro (2012).
Nectin ectodomain structures reveal a canonical adhesive interface.
  Nat Struct Mol Biol, 19, 906-915.
PDB codes: 4fmf 4fmk 4fn0 4fom 4fqp 4frw 4fs0
20808815 A.P.Wright, A.N.Fox, K.G.Johnson, and K.Zinn (2010).
Systematic screening of Drosophila deficiency mutations for embryonic phenotypes and orphan receptor ligands.
  PLoS One, 5, 0.  
19916164 D.Koutsioulis, A.Lyskowski, S.Mäki, E.Guthrie, G.Feller, V.Bouriotis, and P.Heikinheimo (2010).
Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases.
  Protein Sci, 19, 75-84.
PDB codes: 2w5v 2w5w 2w5x
20154452 H.Orimo (2010).
The mechanism of mineralization and the role of alkaline phosphatase in health and disease.
  J Nippon Med Sch, 77, 4.  
20881961 T.Nogi, N.Yasui, E.Mihara, Y.Matsunaga, M.Noda, N.Yamashita, T.Toyofuku, S.Uchiyama, Y.Goshima, A.Kumanogoh, and J.Takagi (2010).
Structural basis for semaphorin signalling through the plexin receptor.
  Nature, 467, 1123-1127.
PDB codes: 3afc 3al8 3al9
19500388 D.Fauvert, I.Brun-Heath, A.S.Lia-Baldini, L.Bellazi, A.Taillandier, J.L.Serre, P.de Mazancourt, and E.Mornet (2009).
Mild forms of hypophosphatasia mostly result from dominant negative effect of severe alleles or from compound heterozygosity for severe and moderate alleles.
  BMC Med Genet, 10, 51.  
19790257 T.S.Kang, and R.C.Stevens (2009).
Structural aspects of therapeutic enzymes to treat metabolic disorders.
  Hum Mutat, 30, 1591-1610.  
19298366 W.Qiao, C.Ellis, J.Steffen, C.Y.Wu, and D.J.Eide (2009).
Zinc status and vacuolar zinc transporters control alkaline phosphatase accumulation and activity in Saccharomyces cerevisiae.
  Mol Microbiol, 72, 320-334.  
18365740 A.I.Vovk, A.L.Chuííko, L.A.Kononets, V.I.u.Tanchuk, I.V.Murav'eva, M.O.Lozinskií, and V.P.Kukhar' (2008).
[Inhibition of alkaline phosphatase by thioureido derivatives of methylenebisphosphonic acid].
  Bioorg Khim, 34, 67-74.  
18576638 A.S.Lipton, R.W.Heck, S.Primak, D.R.McNeill, D.M.Wilson, and P.D.Ellis (2008).
Characterization of Mg2+ binding to the DNA repair protein apurinic/apyrimidic endonuclease 1 via solid-state 25Mg NMR spectroscopy.
  J Am Chem Soc, 130, 9332-9341.  
18925618 B.Simon-Bouy, A.Taillandier, D.Fauvert, I.Brun-Heath, J.L.Serre, C.G.Armengod, M.G.Bialer, M.Mathieu, J.Cousin, D.Chitayat, J.Liebelt, B.Feldman, M.Gérard-Blanluet, S.Körtge-Jung, C.King, H.Laivuori, M.Le Merrer, S.Mehta, C.Jern, S.Sharif, F.Prieur, G.Gillessen-Kaesbach, A.Zankl, and E.Mornet (2008).
Hypophosphatasia: molecular testing of 19 prenatal cases and discussion about genetic counseling.
  Prenat Diagn, 28, 993-998.  
18219546 F.Barvencik, M.Gebauer, T.Schinke, and M.Amling (2008).
Case report: multiple fractures in a patient with mutations of TWIST1 and TNSALP.
  Clin Orthop Relat Res, 466, 990-996.  
17922851 I.Brun-Heath, E.Chabrol, M.Fox, K.Drexler, C.Petit, A.Taillandier, P.De Mazancourt, J.L.Serre, and E.Mornet (2008).
A case of lethal hypophosphatasia providing new insights into the perinatal benign form of hypophosphatasia and expression of the ALPL gene.
  Clin Genet, 73, 245-250.  
18851975 J.G.Zalatan, T.D.Fenn, and D.Herschlag (2008).
Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion.
  J Mol Biol, 384, 1174-1189.
PDB code: 3dyc
18004751 J.W.Torrance, M.W.Macarthur, and J.M.Thornton (2008).
Evolution of binding sites for zinc and calcium ions playing structural roles.
  Proteins, 71, 813-830.  
18058122 M.C.Giocondi, B.Seantier, P.Dosset, P.E.Milhiet, and C.Le Grimellec (2008).
Characterizing the interactions between GPI-anchored alkaline phosphatases and membrane domains by AFM.
  Pflugers Arch, 456, 179-188.  
18724009 N.Sogabe, K.Oda, H.Nakamura, H.Orimo, H.Watanabe, T.Hosoi, and M.Goseki-Sone (2008).
Molecular effects of the tissue-nonspecific alkaline phosphatase gene polymorphism (787T > C) associated with bone mineral density.
  Biomed Res, 29, 213-219.  
17068819 A.Kumar, T.Chatopadhyay, M.Raziuddin, and R.Ralhan (2007).
Discovery of deregulation of zinc homeostasis and its associated genes in esophageal squamous cell carcinoma using cDNA microarray.
  Int J Cancer, 120, 230-242.  
17916236 E.Mornet (2007).
Hypophosphatasia.
  Orphanet J Rare Dis, 2, 40.  
17703464 M.C.Giocondi, F.Besson, P.Dosset, P.E.Milhiet, and C.Le Grimellec (2007).
Temperature-dependent localization of GPI-anchored intestinal alkaline phosphatase in model rafts.
  J Mol Recognit, 20, 531-537.  
16385549 A.Ghosh, Y.Yue, and D.Duan (2006).
Viral serotype and the transgene sequence influence overlapping adeno-associated viral (AAV) vector-mediated gene transfer in skeletal muscle.
  J Gene Med, 8, 298-305.  
16934014 A.Sheikholvaezin, P.Sandström, D.Eriksson, N.Norgren, K.Riklund, and T.Stigbrand (2006).
Optimizing the generation of recombinant single-chain antibodies against placental alkaline phosphatase.
  Hybridoma (Larchmt), 25, 181-192.  
16689578 J.Guthmuller, and D.Simon (2006).
Water solvent effect on the first hyperpolarizability of p-nitrophenol and p-nitrophenylphosphate: a time-dependent density functional study.
  J Chem Phys, 124, 174502.  
  18404473 J.L.Millán (2006).
Alkaline Phosphatases : Structure, substrate specificity and functional relatedness to other members of a large superfamily of enzymes.
  Purinergic Signal, 2, 335-341.  
17212778 M.Nasu, M.Ito, Y.Ishida, N.Numa, K.Komaru, S.Nomura, and K.Oda (2006).
Aberrant interchain disulfide bridge of tissue-nonspecific alkaline phosphatase with an Arg433-->Cys substitution associated with severe hypophosphatasia.
  FEBS J, 273, 5612-5624.  
17253930 M.Spentchian, I.Brun-Heath, A.Taillandier, D.Fauvert, J.L.Serre, B.Simon-Bouy, F.Carvalho, I.Grochova, S.G.Mehta, G.Müller, S.L.Oberstein, G.Ogur, S.Sharif, and E.Mornet (2006).
Characterization of missense mutations and large deletions in the ALPL gene by sequencing and quantitative multiplex PCR of short fragments.
  Genet Test, 10, 252-257.  
16815919 P.Llinas, M.Masella, T.Stigbrand, A.Ménez, E.A.Stura, and M.H.Le Du (2006).
Structural studies of human alkaline phosphatase in complex with strontium: implication for its secondary effect in bones.
  Protein Sci, 15, 1691-1700.
PDB code: 2glq
17489017 S.T.Stinghen, J.F.Moura, P.Zancanella, G.A.Rodrigues, M.A.Pianovski, E.Lalli, D.L.Arnold, J.C.Minozzo, L.G.Callefe, R.C.Ribeiro, and B.C.Figueiredo (2006).
Specific immunoassays for placental alkaline phosphatase as a tumor marker.
  J Biomed Biotechnol, 2006, 56087.  
16372914 D.Saini, M.Kala, V.Jain, and S.Sinha (2005).
Targeting the active site of the placental isozyme of alkaline phosphatase by phage-displayed scFv antibodies selected by a specific uncompetitive inhibitor.
  BMC Biotechnol, 5, 33.  
15824850 M.Goseki-Sone, N.Sogabe, M.Fukushi-Irie, L.Mizoi, H.Orimo, T.Suzuki, H.Nakamura, H.Orimo, and T.Hosoi (2005).
Functional analysis of the single nucleotide polymorphism (787T>C) in the tissue-nonspecific alkaline phosphatase gene associated with BMD.
  J Bone Miner Res, 20, 773-782.  
15885097 T.Harada, I.Koyama, T.Matsunaga, A.Kikuno, T.Kasahara, M.Hassimoto, D.H.Alpers, and T.Komoda (2005).
Characterization of structural and catalytic differences in rat intestinal alkaline phosphatase isozymes.
  FEBS J, 272, 2477-2486.  
16328740 Y.Zhu, X.Y.Song, W.H.Zhao, and Y.X.Zhang (2005).
Effects of magnesium ions on thermal inactivation of alkaline phosphatase.
  Protein J, 24, 479-485.  
15476587 A.Kozlenkov, M.H.Le Du, P.Cuniasse, T.Ny, M.F.Hoylaerts, and J.L.Millán (2004).
Residues determining the binding specificity of uncompetitive inhibitors to tissue-nonspecific alkaline phosphatase.
  J Bone Miner Res, 19, 1862-1872.  
15189884 L.Zhang, R.Buchet, and G.Azzar (2004).
Phosphate binding in the active site of alkaline phosphatase and the interactions of 2-nitrosoacetophenone with alkaline phosphatase-induced small structural changes.
  Biophys J, 86, 3873-3881.  
15333925 M.M.de Backer, S.McSweeney, P.F.Lindley, and E.Hough (2004).
Ligand-binding and metal-exchange crystallographic studies on shrimp alkaline phosphatase.
  Acta Crystallogr D Biol Crystallogr, 60, 1555-1561.
PDB codes: 1shn 1shq
12548282 R.J.Fletcher, B.E.Bishop, R.P.Leon, R.A.Sclafani, C.M.Ogata, and X.S.Chen (2003).
The structure and function of MCM from archaeal M. Thermoautotrophicum.
  Nat Struct Biol, 10, 160-167.
PDB code: 1ltl
11818032 C.C.Denier, A.A.Brisson-Lougarre, G.G.Biasini, J.J.Grozdea, and D.D.Fournier (2002).
Kinetic comparison of tissue non-specific and placental human alkaline phosphatases expressed in baculovirus infected cells: application to screening for Down's syndrome.
  BMC Biochem, 3, 2.  
11857742 C.Wennberg, A.Kozlenkov, S.Di Mauro, N.Fröhlander, L.Beckman, M.F.Hoylaerts, and J.L.Millán (2002).
Structure, genomic DNA typing, and kinetic characterization of the D allozyme of placental alkaline phosphatase (PLAP/ALPP).
  Hum Mutat, 19, 258-267.  
12440695 F.J.Sharom, and M.T.Lehto (2002).
Glycosylphosphatidylinositol-anchored proteins: structure, function, and cleavage by phosphatidylinositol-specific phospholipase C.
  Biochem Cell Biol, 80, 535-549.  
12162492 S.Di Mauro, T.Manes, L.Hessle, A.Kozlenkov, J.M.Pizauro, M.F.Hoylaerts, and J.L.Millán (2002).
Kinetic characterization of hypophosphatasia mutations with physiological substrates.
  J Bone Miner Res, 17, 1383-1391.  
11721007 H.C.Hung, and G.G.Chang (2001).
Multiple unfolding intermediates of human placental alkaline phosphatase in equilibrium urea denaturation.
  Biophys J, 81, 3456-3471.  
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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