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PDBsum entry 1j9l

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protein ligands metals Protein-protein interface(s) links
Unknown function PDB id
1j9l
Jmol
Contents
Protein chains
247 a.a. *
Ligands
VO4 ×2
EPE
Metals
_CA ×3
Waters ×282
* Residue conservation analysis
PDB id:
1j9l
Name: Unknown function
Title: Crystal structure of sure protein from t.Maritima in complex vanadate
Structure: Stationary phase survival protein. Chain: a, b. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.199     R-free:   0.241
Authors: S.W.Suh,J.Y.Lee,J.E.Kwak,J.Moon
Key ref:
J.Y.Lee et al. (2001). Crystal structure and functional analysis of the SurE protein identify a novel phosphatase family. Nat Struct Biol, 8, 789-794. PubMed id: 11524683 DOI: 10.1038/nsb0901-789
Date:
28-May-01     Release date:   12-Sep-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P96112  (SURE_THEMA) -  5'-nucleotidase SurE
Seq:
Struc:
247 a.a.
247 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nsb0901-789 Nat Struct Biol 8:789-794 (2001)
PubMed id: 11524683  
 
 
Crystal structure and functional analysis of the SurE protein identify a novel phosphatase family.
J.Y.Lee, J.E.Kwak, J.Moon, S.H.Eom, E.C.Liong, J.D.Pedelacq, J.Berendzen, S.W.Suh.
 
  ABSTRACT  
 
Homologs of the Escherichia coli surE gene are present in many eubacteria and archaea. Despite the evolutionary conservation, little information is available on the structure and function of their gene products. We have determined the crystal structure of the SurE protein from Thermotoga maritima. The structure reveals the dimeric arrangement of the subunits and an active site around a bound metal ion. We also demonstrate that the SurE protein exhibits a divalent metal ion-dependent phosphatase activity that is inhibited by vanadate or tungstate. In the vanadate- and tungstate-complexed structures, the inhibitors bind adjacent to the divalent metal ion. Our structural and functional analyses identify the SurE proteins as a novel family of metal ion-dependent phosphatases.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The overall fold of T. maritima SurE. a, Stereo ribbon diagram of the SurE monomer. -helices are colored purple and -strands, cyan. The divalent metal ion is displayed as a blue ball and the residues coordinating the metal ion (Asp 8, Asp 9, Ser 39 and Asn 95) are indicated. b, Stereo ribbon diagram of the SurE dimer in complex with divalent metal ions (spheres) and tungstate ions. -helices and -strands in one monomer are colored purple and cyan, respectively. Those in the other monomer are colored in red and green, respectively. Drawn with the programs MOLSCRIPT24 and RASTER3D^25.
Figure 3.
Figure 3. Stereo views of the divalent metal ion binding site. a, Final (2F[o] - F[c]) electron density map around the divalent metal ion binding site in the native structure. The map was calculated using 20 -1.9 data and was contoured at 1.2 . Drawn with the program BOBSCRIPT26. Views are of the divalent metal ion (blue spheres) and inhibitor binding. b, The native structure. c, The tungstate-complex structure. d, The vanadate-complex structure. Atoms of carbon, nitrogen and oxygen are in green, blue and red, respectively. Close contacts within 3.2 are denoted by dotted lines with distances in . (c) and (d) also show the electron density of the inhibitors in the omit F[o] - F[c] maps.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 789-794) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19943903 D.R.Buelow, and T.L.Raivio (2010).
Three (and more) component regulatory systems - auxiliary regulators of bacterial histidine kinases.
  Mol Microbiol, 75, 547-566.  
20192973 N.R.Williamson, P.M.Commander, and G.P.Salmond (2010).
Quorum sensing-controlled Evr regulates a conserved cryptic pigment biosynthetic cluster and a novel phenomycin-like locus in the plant pathogen, Pectobacterium carotovorum.
  Environ Microbiol, 12, 1811-1827.  
21038358 S.K.Sekatskii, M.Favre, G.Dietler, A.G.Mikhailov, D.V.Klinov, S.V.Lukash, and S.M.Deyev (2010).
Force spectroscopy of barnase-barstar single molecule interaction.
  J Mol Recognit, 23, 583-588.  
18567005 M.D.Altman, J.P.Bardhan, J.K.White, and B.Tidor (2009).
Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements.
  J Comput Chem, 30, 132-153.  
19836334 S.Yamada, H.Sugimoto, M.Kobayashi, A.Ohno, H.Nakamura, and Y.Shiro (2009).
Structure of PAS-linked histidine kinase and the response regulator complex.
  Structure, 17, 1333-1344.
PDB codes: 3a0r 3a0s 3a0t 3a0u 3a0v 3a0w 3a0x 3a0y 3a0z 3a10
  18323612 A.M.Gonçalves, A.T.Rêgo, M.Thomaz, F.J.Enguita, and M.A.Carrondo (2008).
Expression, purification, crystallization and preliminary X-ray characterization of two crystal forms of stationary-phase survival E protein from Campylobacter jejuni.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 213-216.  
19021761 A.Pappachan, H.S.Savithri, and M.R.Murthy (2008).
Structural and functional studies on a mesophilic stationary phase survival protein (Sur E) from Salmonella typhimurium.
  FEBS J, 275, 5855-5864.
PDB codes: 2v4n 2v4o
17729291 M.D.Altman, E.A.Nalivaika, M.Prabu-Jeyabalan, C.A.Schiffer, and B.Tidor (2008).
Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease.
  Proteins, 70, 678-694.
PDB codes: 2nxd 2nxl 2nxm
18560010 Q.Cui, and M.Karplus (2008).
Allostery and cooperativity revisited.
  Protein Sci, 17, 1295-1307.  
18441234 Y.Urakubo, T.Ikura, and N.Ito (2008).
Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation.
  Protein Sci, 17, 1055-1065.
PDB code: 2za4
18247352 Y.Zhao, W.Li, J.Zeng, G.Liu, and Y.Tang (2008).
Insights into the interactions between HIV-1 integrase and human LEDGF/p75 by molecular dynamics simulation and free energy calculation.
  Proteins, 72, 635-645.  
17376072 M.Kojima, R.Kubo, T.Yakushi, M.Homma, and I.Kawagishi (2007).
The bidirectional polar and unidirectional lateral flagellar motors of Vibrio alginolyticus are controlled by a single CheY species.
  Mol Microbiol, 64, 57-67.  
17019722 M.S.Formaneck, and Q.Cui (2006).
The use of a generalized born model for the analysis of protein conformational transitions: a comparative study with explicit solvent simulations for chemotaxis Y protein (CheY).
  J Comput Chem, 27, 1923-1943.  
16988958 S.Bhat, T.Sulea, and E.O.Purisima (2006).
Coupled atomic charge selectivity for optimal ligand-charge distributions at protein binding sites.
  J Comput Chem, 27, 1899-1907.  
16257567 C.L.Vizcarra, and S.L.Mayo (2005).
Electrostatics in computational protein design.
  Curr Opin Chem Biol, 9, 622-626.  
16001428 D.F.Green, and B.Tidor (2005).
Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface.
  Proteins, 60, 644-657.  
15808744 E.Kuznetsova, M.Proudfoot, S.A.Sanders, J.Reinking, A.Savchenko, C.H.Arrowsmith, A.M.Edwards, and A.F.Yakunin (2005).
Enzyme genomics: Application of general enzymatic screens to discover new enzymes.
  FEMS Microbiol Rev, 29, 263-279.  
15808745 K.Stephenson, and R.J.Lewis (2005).
Molecular insights into the initiation of sporulation in Gram-positive bacteria: new technologies for an old phenomenon.
  FEMS Microbiol Rev, 29, 281-301.  
15998643 M.R.Buddha, and B.R.Crane (2005).
Structures of tryptophanyl-tRNA synthetase II from Deinococcus radiodurans bound to ATP and tryptophan. Insight into subunit cooperativity and domain motions linked to catalysis.
  J Biol Chem, 280, 31965-31973.
PDB codes: 1yid 2a4m
15880257 X.H.Cai, Q.Zhang, S.Y.Shi, and D.F.Ding (2005).
Searching for potential drug targets in two-component and phosphorelay signal-transduction systems using three-dimensional cluster analysis.
  Acta Biochim Biophys Sin (Shanghai), 37, 293-302.  
15887221 Y.Shaul, and G.Schreiber (2005).
Exploring the charge space of protein-protein association: a proteomic study.
  Proteins, 60, 341-352.  
15255896 K.Muchová, R.J.Lewis, D.Perecko, J.A.Brannigan, J.C.Ladds, A.Leech, A.J.Wilkinson, and I.Barák (2004).
Dimer-induced signal propagation in Spo0A.
  Mol Microbiol, 53, 829-842.  
15036162 T.Kortemme, and D.Baker (2004).
Computational design of protein-protein interactions.
  Curr Opin Chem Biol, 8, 91-97.  
12668646 H.Kavermann, B.P.Burns, K.Angermuller, S.Odenbreit, W.Fischer, K.Melchers, and R.Haas (2003).
Identification and characterization of Helicobacter pylori genes essential for gastric colonization.
  J Exp Med, 197, 813-822.  
12940980 J.A.Hubbard, L.K.MacLachlan, G.W.King, J.J.Jones, and A.P.Fosberry (2003).
Nuclear magnetic resonance spectroscopy reveals the functional state of the signalling protein CheY in vivo in Escherichia coli.
  Mol Microbiol, 49, 1191-1200.  
12925525 J.E.Domínguez, M.C.Muñoz, D.Zafra, I.Sanchez-Perez, S.Baqué, M.Caron, C.Mercurio, A.Barberà, R.Perona, R.Gomis, and J.J.Guinovart (2003).
The antidiabetic agent sodium tungstate activates glycogen synthesis through an insulin receptor-independent pathway.
  J Biol Chem, 278, 42785-42794.  
14503005 T.Kakimoto (2003).
Perception and signal transduction of cytokinins.
  Annu Rev Plant Biol, 54, 605-627.  
12453214 T.Yoshida, L.Qin, and M.Inouye (2002).
Formation of the stoichiometric complex of EnvZ, a histidine kinase, with its response regulator, OmpR.
  Mol Microbiol, 46, 1273-1282.  
11406410 A.H.West, and A.M.Stock (2001).
Histidine kinases and response regulator proteins in two-component signaling systems.
  Trends Biochem Sci, 26, 369-376.  
11297935 T.Simonson (2001).
Macromolecular electrostatics: continuum models and their growing pains.
  Curr Opin Struct Biol, 11, 243-252.  
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.