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Hydrolase PDB id
1hpu
Jmol
Contents
Protein chains
525 a.a. *
Ligands
A12 ×4
Metals
_MN ×8
Waters ×1219
* Residue conservation analysis
PDB id:
1hpu
Name: Hydrolase
Title: 5'-nucleotidase (closed form), complex with ampcp
Structure: 5'-nucleotidase. Chain: a, b, c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: usha. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.85Å     R-factor:   0.207     R-free:   0.234
Authors: T.Knoefel,N.Straeter
Key ref:
T.Knöfel and N.Sträter (2001). Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures. J Mol Biol, 309, 239-254. PubMed id: 11491293 DOI: 10.1006/jmbi.2001.4656
Date:
13-Dec-00     Release date:   20-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07024  (USHA_ECOLI) -  Protein UshA
Seq:
Struc: 		 
Seq:
Struc: 		550 a.a.
525 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.3.1.3.5  - 5'-nucleotidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A 5'-ribonucleotide + H2O = a ribonucleoside + phosphate
5'-ribonucleotide
Bound ligand (Het Group name = A12)
matches with 41.00% similarity 		+ H(2)O
 = ribonucleoside
 + phosphate
   Enzyme class 3: E.C.3.6.1.45  - UDP-sugar diphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: UDP-sugar + H2O = UMP + alpha-D-aldose 1-phosphate
UDP-sugar
 + H(2)O
 =
UMP
Bound ligand (Het Group name = A12)
matches with 60.00% similarity 		+ alpha-D-aldose 1-phosphate
      Cofactor: Divalent cation
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     nucleotide catabolic process   1 term 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.4656 J Mol Biol 309:239-254 (2001)
PubMed id: 11491293  
 
 
Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.
T.Knöfel, N.Sträter.
 
  ABSTRACT  
 
5'-Nucleotidase belongs to a large superfamily of distantly related dinuclear metallophosphatases including the Ser/Thr protein phosphatases and purple acid phosphatases. The protein undergoes a 96 degrees domain rotation between an open (inactive) and a closed (active) enzyme form. Complex structures of the closed form with the products adenosine and phosphate, and with the substrate analogue inhibitor alpha,beta-methylene ADP, have been determined at 2.1 A and 1.85 A resolution, respectively. In addition, a complex of the open form of 5'-nucleotidase with ATP was analyzed at a resolution of 1.7 A. These structures show that the adenosine group binds to a specific binding pocket of the C-terminal domain. The adenine ring is stacked between Phe429 and Phe498. The N-terminal domain provides the ligands to the dimetal cluster and the conserved His117, which together form the catalytic core structure. However, the three C-terminal arginine residues 375, 379 and 410, which are involved in substrate binding, may also play a role in transition-state stabilization. The beta-phosphate group of the inhibitor is terminally coordinated to the site 2 metal ion. The site 1 metal ion coordinates a water molecule which is in an ideal position for a nucleophilic attack on the phosphorus atom, assuming an in-line mechanism of phosphoryl transfer. Another water molecule bridges the two metal ions.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Superposition of AMPCP and surrounding protein residues of molecules B and C of crystal form IV. The two molecules have been superimposed based on the C^a residues of the C-terminal domains (361-550). The protein residues of conformer C are shown in yellow and the AMPCP molecule bound to it in red. Residues of the N-terminal domain of conformer B are shown in cyan and those of the C-terminal domain in blue. The AMPCP inhibitor bound to conformer B is colored green. The carbonyl oxygen atom of Ile178 is depicted in red. 		Figure 7.
Figure 7. Superposition of the active site structures of the closed conformation of E. coli 5'-NT (green), kidney bean purple acid phosphatase (blue, PDB code 4KBP), human calcineurin (yellow, PP-2B, PDB code 1AUI), and rabbit protein phosphatase 1 (red, PDB code 1FJM). The structures were superimposed on the basis of the coordinates of the two metal ions and the C^a atoms of the conserved metal ligands and the catalytic histidine residue.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 309, 239-254) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20351782 G.Caljon, K.De Ridder, P.De Baetselier, M.Coosemans, and J.Van Den Abbeele (2010).
Identification of a tsetse fly salivary protein with dual inhibitory action on human platelet aggregation.
  PLoS One, 5, e9671.  
19535341 V.Sauvé, P.Roversi, K.J.Leath, E.F.Garman, R.Antrobus, S.M.Lea, and B.C.Berks (2009).
Mechanism for the Hydrolysis of a Sulfur-Sulfur Bond Based on the Crystal Structure of the Thiosulfohydrolase SoxB.
  J Biol Chem, 284, 21707-21718.
PDB codes: 2wdc 2wdd 2wde 2wdf
19808256 V.Thammavongsa, J.W.Kern, D.M.Missiakas, and O.Schneewind (2009).
Staphylococcus aureus synthesizes adenosine to escape host immune responses.
  J Exp Med, 206, 2417-2427.  
17847097 D.H.Shin, M.Proudfoot, H.J.Lim, I.K.Choi, H.Yokota, A.F.Yakunin, R.Kim, and S.H.Kim (2008).
Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans.
  Proteins, 70, 1000-1009.
PDB code: 1t70
18641143 I.Alves-Pereira, J.Canales, A.Cabezas, P.M.Cordero, M.J.Costas, and J.C.Cameselle (2008).
CDP-alcohol hydrolase, a very efficient activity of the 5'-nucleotidase/UDP-sugar hydrolase encoded by the ushA gene of Yersinia intermedia and Escherichia coli.
  J Bacteriol, 190, 6153-6161.  
18353368 M.D.Zimmerman, M.Proudfoot, A.Yakunin, and W.Minor (2008).
Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.
  J Mol Biol, 378, 215-226.
PDB codes: 2paq 2par 2pau
18757371 N.Keppetipola, and S.Shuman (2008).
A Phosphate-binding Histidine of Binuclear Metallophosphodiesterase Enzymes Is a Determinant of 2',3'-Cyclic Nucleotide Phosphodiesterase Activity.
  J Biol Chem, 283, 30942-30949.  
19030623 O.Taran, F.Medrano, and A.K.Yatsimirsky (2008).
Rapid hydrolysis of model phosphate diesters by alkaline-earth cations in aqueous DMSO: speciation and kinetics.
  Dalton Trans, 0, 6609-6618.  
17586769 D.J.Miller, L.Shuvalova, E.Evdokimova, A.Savchenko, A.F.Yakunin, and W.F.Anderson (2007).
Structural and biochemical characterization of a novel Mn2+-dependent phosphodiesterase encoded by the yfcE gene.
  Protein Sci, 16, 1338-1348.  
  18404437 J.K.Crane, I.Shulgina, and T.M.Naeher (2007).
Ecto-5'-nucleotidase and intestinal ion secretion by enteropathogenic Escherichia coli.
  Purinergic Signal, 3, 233-246.  
16838328 D.Kumaran, J.B.Bonanno, S.K.Burley, and S.Swaminathan (2006).
Crystal structure of phosphatidylglycerophosphatase (PGPase), a putative membrane-bound lipid phosphatase, reveals a novel binuclear metal binding site and two "proton wires".
  Proteins, 64, 851-862.
PDB code: 1y9i
16675457 N.Keppetipola, and S.Shuman (2006).
Distinct enzymic functional groups are required for the phosphomonoesterase and phosphodiesterase activities of Clostridium thermocellum polynucleotide kinase/phosphatase.
  J Biol Chem, 281, 19251-19259.  
18404474 N.Sträter (2006).
Ecto-5'-nucleotidase: Structure function relationships.
  Purinergic Signal, 2, 343-350.  
15965486 B.M.Collins, C.F.Skinner, P.J.Watson, M.N.Seaman, and D.J.Owen (2005).
Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly.
  Nat Struct Mol Biol, 12, 594-602.
PDB codes: 1z2w 1z2x
15505785 C.H.Schein, B.Zhou, N.Oezguen, V.S.Mathura, and W.Braun (2005).
Molego-based definition of the architecture and specificity of metal-binding sites.
  Proteins, 58, 200-210.  
15963349 S.A.Hunsucker, B.S.Mitchell, and J.Spychala (2005).
The 5'-nucleotidases as regulators of nucleotide and drug metabolism.
  Pharmacol Ther, 107, 1.  
14985353 E.Faudry, S.P.Lozzi, J.M.Santana, M.D'Souza-Ault, S.Kieffer, C.R.Felix, C.A.Ricart, M.V.Sousa, T.Vernet, and A.R.Teixeira (2004).
Triatoma infestans apyrases belong to the 5'-nucleotidase family.
  J Biol Chem, 279, 19607-19613.  
14699168 J.A.Roberts, and R.J.Evans (2004).
ATP binding at human P2X1 receptors. Contribution of aromatic and basic amino acids revealed using mutagenesis and partial agonists.
  J Biol Chem, 279, 9043-9055.  
15375722 P.Zimmermann, B.Regierer, J.Kossmann, E.Frossard, N.Amrhein, and M.Bucher (2004).
Differential expression of three purple acid phosphatases from potato.
  Plant Biol (Stuttg), 6, 519-528.  
15215524 R.Schultz-Heienbrok, T.Maier, and N.Sträter (2004).
Trapping a 96 degrees domain rotation in two distinct conformations by engineered disulfide bridges.
  Protein Sci, 13, 1811-1822.
PDB codes: 1oi8 1oid 1oie
14711669 S.Y.McLoughlin, C.Jackson, J.W.Liu, and D.L.Ollis (2004).
Growth of Escherichia coli coexpressing phosphotriesterase and glycerophosphodiester phosphodiesterase, using paraoxon as the sole phosphorus source.
  Appl Environ Microbiol, 70, 404-412.  
12947102 V.Bianchi, and J.Spychala (2003).
Mammalian 5'-nucleotidases.
  J Biol Chem, 278, 46195-46198.  
12866051 Y.Y.Kuttner, V.Sobolev, A.Raskind, and M.Edelman (2003).
A consensus-binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine-containing complexes.
  Proteins, 52, 400-411.  
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.