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PDBsum entry 1ush

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protein ligands metals links
Hydrolase PDB id
1ush
Jmol
Contents
Protein chain
515 a.a. *
Ligands
CO3
SO4 ×4
Metals
_ZN ×2
Waters ×585
* Residue conservation analysis
PDB id:
1ush
Name: Hydrolase
Title: 5'-nucleotidase from e. Coli
Structure: 5'-nucleotidase. Chain: a. Synonym: udp-sugar hydrolase. Engineered: yes. Other_details: complex with carbonate
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: usha. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.73Å     R-factor:   0.180     R-free:   0.219
Authors: T.Knofel,N.Strater
Key ref:
T.Knöfel and N.Sträter (1999). X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site. Nat Struct Biol, 6, 448-453. PubMed id: 10331872 DOI: 10.1038/8253
Date:
16-Sep-98     Release date:   15-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07024  (USHA_ECOLI) -  Protein UshA
Seq:
Struc:
 
Seq:
Struc:
550 a.a.
515 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
+ 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
+ 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!
  Biological process     nucleotide catabolic process   1 term 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1038/8253 Nat Struct Biol 6:448-453 (1999)
PubMed id: 10331872  
 
 
X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site.
T.Knöfel, N.Sträter.
 
  ABSTRACT  
 
The crystal structure of 5'-nucleotidase (5'-NT) from E. coli, also known as UDP-sugar hydrolase, has been determined at 1.7 A resolution. Two zinc ions are present in the active site, which is located in a cleft between two domains. The dimetal center and a catalytic Asp-His dyad are the main players in the catalytic mechanism. Structure-based sequence comparisons show that the structure also provides a model for animal 5'-NTs, which together with other ectonucleotidases terminate the action of nucleotides as extracellular signaling substances in the nervous system.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Active-site region. a, Stereo view of an omit electron density map (|F[o] - F[c]| * [c]; residues shown are omitted from the calculation of F[c] and [c], in green) and anomalous density map (|F^+[NATANO] − F^− [NATANO] | * [c] in purple; see Table 1) of the two zinc ions (Zn1 on the left side) with the protein ligands, a (bi)carbonate ion, and His 117. b, Selected residues near the di-zinc center. The backbone fold of the N- and C-terminal domains is shown in green and blue, respectively. c, Schematic representation of the dizinc center, the carbonate ion, and the catalytic Asp- His dyad. In the orthorhombic crystal form, two water molecules bind in place of the carbonate ion. The number of digits given for the interatomic distances does not necessarily reflect the accuracy of the numbers. Prepared using BOBSCRIPT^34 (a) and MOLSCRIPT^30 and Raster3D^31 (b).
Figure 4.
Figure 4. Superposition of the active-site structures of E. coli 5'-NT (green), kidney bean purple acid phosphatase (blue, PDB code 4KBP^12, ^13), human calcineurin (yellow, PP-2B, PDB code 1AUI^15), and rabbit protein phosphatase 1 (red, PDB code 1FJM^14). The structures were superimposed on the basis of the coordinates of the two metal ions and of the C atoms of the conserved metal ligands and the catalytic histidine. Most residues are labeled only for the 5'-NT structure (in green labels). This figure was generated using MOLSCRIPT^30 and Raster3D^31.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 448-453) copyright 1999.  
  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).
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20440438 Q.Chu, D.A.Medvetz, M.J.Panzner, and Y.Pang (2010).
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  Dalton Trans, 39, 5254-5259.  
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
  18678932 C.J.Jackson, K.S.Hadler, P.D.Carr, A.J.Oakley, S.Yip, G.Schenk, and D.L.Ollis (2008).
Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 681-685.
PDB codes: 2zo9 2zoa
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.  
18458329 M.Zebisch, and N.Sträter (2008).
Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling.
  Proc Natl Acad Sci U S A, 105, 6882-6887.
PDB codes: 3cj1 3cj7 3cj9 3cja
17895995 K.S.Makarova, M.V.Omelchenko, E.K.Gaidamakova, V.Y.Matrosova, A.Vasilenko, M.Zhai, A.Lapidus, A.Copeland, E.Kim, M.Land, K.Mavrommatis, S.Pitluck, P.M.Richardson, C.Detter, T.Brettin, E.Saunders, B.Lai, B.Ravel, K.M.Kemner, Y.I.Wolf, A.Sorokin, A.V.Gerasimova, M.S.Gelfand, J.K.Fredrickson, E.V.Koonin, and M.J.Daly (2007).
Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.
  PLoS ONE, 2, e955.  
16522806 B.A.Manjasetty, K.Büssow, M.Fieber-Erdmann, Y.Roske, J.Gobom, C.Scheich, F.Götz, F.H.Niesen, and U.Heinemann (2006).
Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold.
  Protein Sci, 15, 914-920.
PDB code: 1xcr
  16820687 C.J.Jackson, P.D.Carr, H.K.Kim, J.W.Liu, and D.L.Ollis (2006).
The purification, crystallization and preliminary diffraction of a glycerophosphodiesterase from Enterobacter aerogenes.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 659-661.  
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
18404474 N.Sträter (2006).
Ecto-5'-nucleotidase: Structure function relationships.
  Purinergic Signal, 2, 343-350.  
  18404494 , (2006).
Invited Lectures : Overviews Purinergic signalling: past, present and future.
  Purinergic Signal, 2, 1.  
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.  
16085822 D.Rittmann, U.Sorger-Herrmann, and V.F.Wendisch (2005).
Phosphate starvation-inducible gene ushA encodes a 5' nucleotidase required for growth of Corynebacterium glutamicum on media with nucleotides as the phosphorus source.
  Appl Environ Microbiol, 71, 4339-4344.  
15788412 D.Wang, M.Guo, Z.Liang, J.Fan, Z.Zhu, J.Zang, Z.Zhu, X.Li, M.Teng, L.Niu, Y.Dong, and P.Liu (2005).
Crystal structure of human vacuolar protein sorting protein 29 reveals a phosphodiesterase/nuclease-like fold and two protein-protein interaction sites.
  J Biol Chem, 280, 22962-22967.
PDB code: 1w24
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.  
  15343381 H.Castrop, Y.Huang, S.Hashimoto, D.Mizel, P.Hansen, F.Theilig, S.Bachmann, C.Deng, J.Briggs, and J.Schnermann (2004).
Impairment of tubuloglomerular feedback regulation of GFR in ecto-5'-nucleotidase/CD73-deficient mice.
  J Clin Invest, 114, 634-642.  
15489502 M.Proudfoot, E.Kuznetsova, G.Brown, N.N.Rao, M.Kitagawa, H.Mori, A.Savchenko, and A.F.Yakunin (2004).
General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG.
  J Biol Chem, 279, 54687-54694.  
15557261 M.Seto, M.Whitlow, M.A.McCarrick, S.Srinivasan, Y.Zhu, R.Pagila, R.Mintzer, D.Light, A.Johns, and J.A.Meurer-Ogden (2004).
A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase.
  Protein Sci, 13, 3172-3186.
PDB code: 1x9o
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
15128743 S.Chen, A.F.Yakunin, E.Kuznetsova, D.Busso, R.Pufan, M.Proudfoot, R.Kim, and S.H.Kim (2004).
Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii.
  J Biol Chem, 279, 31854-31862.
PDB codes: 1s3l 1s3m 1s3n
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.  
12833551 D.Kumaran, S.Eswaramoorthy, S.E.Gerchman, H.Kycia, F.W.Studier, and S.Swaminathan (2003).
Crystal structure of a putative CN hydrolase from yeast.
  Proteins, 52, 283-291.
PDB code: 1f89
12715899 R.Napieralski, B.Kempkes, and W.Gutensohn (2003).
Evidence for coordinated induction and repression of ecto-5'-nucleotidase (CD73) and the A2a adenosine receptor in a human B cell line.
  Biol Chem, 384, 483-487.  
12947102 V.Bianchi, and J.Spychala (2003).
Mammalian 5'-nucleotidases.
  J Biol Chem, 278, 46195-46198.  
12352955 A.Rinaldo-Matthis, C.Rampazzo, P.Reichard, V.Bianchi, and P.Nordlund (2002).
Crystal structure of a human mitochondrial deoxyribonucleotidase.
  Nat Struct Biol, 9, 779-787.
PDB code: 1mh9
12167635 B.U.Failer, N.Braun, and H.Zimmermann (2002).
Cloning, expression, and functional characterization of a Ca(2+)-dependent endoplasmic reticulum nucleoside diphosphatase.
  J Biol Chem, 277, 36978-36986.  
11863431 F.Verté, V.Kostanjevecki, L.De Smet, T.E.Meyer, M.A.Cusanovich, and J.J.Van Beeumen (2002).
Identification of a thiosulfate utilization gene cluster from the green phototrophic bacterium Chlorobium limicola.
  Biochemistry, 41, 2932-2945.  
12000771 K.J.Babinski, S.J.Kanjilal, and C.R.Raetz (2002).
Accumulation of the lipid A precursor UDP-2,3-diacylglucosamine in an Escherichia coli mutant lacking the lpxH gene.
  J Biol Chem, 277, 25947-25956.  
11567011 C.Appia-Ayme, P.J.Little, Y.Matsumoto, A.P.Leech, and B.C.Berks (2001).
Cytochrome complex essential for photosynthetic oxidation of both thiosulfate and sulfide in Rhodovulum sulfidophilum.
  J Bacteriol, 183, 6107-6118.  
10931179 C.Fini, A.Amoresano, A.Andolfo, S.D'auria, A.Floridi, S.Paolini, and P.Pucci (2000).
Mass spectrometry study of ecto-5'-nucleotidase from bull seminal plasma.
  Eur J Biochem, 267, 4978-4987.  
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.