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PDBsum entry 1k7h

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1k7h
Jmol
Contents
Protein chains
476 a.a. *
Ligands
NAG ×2
SO4 ×6
MAE ×3
Metals
_ZN ×6
Waters ×548
* Residue conservation analysis
PDB id:
1k7h
Name: Hydrolase
Title: Crystal structure of shrimp alkaline phosphatase
Structure: Alkaline phosphatase. Chain: a, b. Ec: 3.1.3.1
Source: Pandalus borealis. Northern shrimp. Organism_taxid: 6703
Biol. unit: Dimer (from PQS)
Resolution:
1.92Å     R-factor:   0.200     R-free:   0.227
Authors: M.E.De Backer,S.Mc Sweeney,H.B.Rasmussen,B.W.Riise,P.Lindley
Key ref:
M.de Backer et al. (2002). The 1.9 A crystal structure of heat-labile shrimp alkaline phosphatase. J Mol Biol, 318, 1265-1274. PubMed id: 12083516 DOI: 10.1016/S0022-2836(02)00035-9
Date:
19-Oct-01     Release date:   31-Jul-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9BHT8  (Q9BHT8_PANBO) -  Alkaline phosphatase (Fragment)
Seq:
Struc:
475 a.a.
476 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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
      Cofactor: Magnesium; Zinc
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(02)00035-9 J Mol Biol 318:1265-1274 (2002)
PubMed id: 12083516  
 
 
The 1.9 A crystal structure of heat-labile shrimp alkaline phosphatase.
M.de Backer, S.McSweeney, H.B.Rasmussen, B.W.Riise, P.Lindley, E.Hough.
 
  ABSTRACT  
 
Alkaline phosphatases are non-specific phosphomonoesterases that are distributed widely in species ranging from bacteria to man. This study has concentrated on the tissue-nonspecific alkaline phosphatase from arctic shrimps (shrimp alkaline phosphatase, SAP). Originating from a cold-active species, SAP is thermolabile and is used widely in vitro, e.g. to dephosphorylate DNA or dNTPs, since it can be inactivated by a short rise in temperature. Since alkaline phosphatases are zinc-containing enzymes, a multiwavelength anomalous dispersion (MAD) experiment was performed on the zinc K edge, which led to the determination of the structure to a resolution of 1.9 A. Anomalous data clearly showed the presence of a zinc triad in the active site, whereas alkaline phosphatases usually contain two zinc and one magnesium ion per monomer. SAP shares the core, an extended beta-sheet flanked by alpha-helices, and a metal triad with the currently known alkaline phosphatase structures (Escherichia coli structures and a human placental structure). Although SAP lacks some features specific for the mammalian enzyme, their backbones are very similar and may therefore be typical for other higher organisms. Furthermore, SAP possesses a striking feature that the other structures lack: surface potential representations show that the enzyme's net charge of -80 is distributed such that the surface is predominantly negatively charged, except for the positively charged active site. The negatively charged substrate must therefore be directed strongly towards the active site. It is generally accepted that optimization of the electrostatics is one of the characteristics related to cold-adaptation. SAP demonstrates this principle very clearly.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Superposition of SAP (coloured by atom) and PLAP (yellow), showing Arg162 in the active site, which has a different conformation in the two structures. The Figure was prepared with MOLSCRIPT.
Figure 5.
Figure 5. Surface potential representation, prepared with GRASP,[48] of (a) SAP, (b) PLAP and (c) ECAP, with potentials ranging from -15 (blue) to +15 (red).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 1265-1274) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153741 M.W.Wojewodzic, M.Kyle, J.J.Elser, D.O.Hessen, and T.Andersen (2011).
Joint effect of phosphorus limitation and temperature on alkaline phosphatase activity and somatic growth in Daphnia magna.
  Oecologia, 165, 837-846.  
  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
20057143 H.Tsuruta, B.Mikami, T.Higashi, and Y.Aizono (2010).
Crystal structure of cold-active alkaline phosphatase from the psychrophile Shewanella sp.
  Biosci Biotechnol Biochem, 74, 69-74.
PDB code: 3a52
19497047 J.Dancourt, and C.Barlowe (2009).
Erv26p-dependent export of alkaline phosphatase from the ER requires lumenal domain recognition.
  Traffic, 10, 1006-1018.  
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.  
18404270 A.Muhlia-Almazán, A.Sánchez-Paz, and F.L.García-Carreño (2008).
Invertebrate trypsins: a review.
  J Comp Physiol [B], 178, 655-672.  
19011975 C.L.Goonasekara, and D.H.Heeley (2008).
Conformational properties of striated muscle tropomyosins from some salmonid fishes.
  J Muscle Res Cell Motil, 29, 135-143.  
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
18294135 L.P.Xie, G.R.Xu, W.Z.Cao, J.Zhang, and R.Q.Zhang (2008).
An essential tryptophan residue in alkaline phosphatase from pearl oyster (Pinctada fucata).
  Biochemistry (Mosc), 73, 87-91.  
17697122 D.Tronelli, E.Maugini, F.Bossa, and S.Pascarella (2007).
Structural adaptation to low temperatures--analysis of the subunit interface of oligomeric psychrophilic enzymes.
  FEBS J, 274, 4595-4608.  
17624576 L.P.Xie, Y.T.Wu, Y.P.Dai, Q.Li, and R.Q.Zhang (2007).
A novel glycosylphosphatidylinositol-anchored alkaline phosphatase dwells in the hepatic duct of the pearl oyster, Pinctada fucata.
  Mar Biotechnol (NY), 9, 613-623.  
16756497 K.S.Siddiqui, and R.Cavicchioli (2006).
Cold-adapted enzymes.
  Annu Rev Biochem, 75, 403-433.  
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
15805593 G.A.Leonard, G.Sainz, M.M.de Backer, and S.McSweeney (2005).
Automatic structure determination based on the single-wavelength anomalous diffraction technique away from an absorption edge.
  Acta Crystallogr D Biol Crystallogr, 61, 388-396.  
15833276 H.T.Chen, L.P.Xie, Z.Y.Yu, G.R.Xu, and R.Q.Zhang (2005).
Chemical modification studies on alkaline phosphatase from pearl oyster (Pinctada fucata): a substrate reaction course analysis and involvement of essential arginine and lysine residues at the active site.
  Int J Biochem Cell Biol, 37, 1446-1457.  
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.  
  16233714 A.Hoyoux, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.L.Huston, J.C.Marx, G.Sonan, Y.Zeng, G.Feller, and C.Gerday (2004).
Extreme catalysts from low-temperature environments.
  J Biosci Bioeng, 98, 317-330.  
14975528 D.Georlette, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.Hoyoux, J.C.Marx, G.Sonan, G.Feller, and C.Gerday (2004).
Some like it cold: biocatalysis at low temperatures.
  FEMS Microbiol Rev, 28, 25-42.  
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
15035024 G.Feller, and C.Gerday (2003).
Psychrophilic enzymes: hot topics in cold adaptation.
  Nat Rev Microbiol, 1, 200-208.  
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.