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PDBsum entry 1j97

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1j97
Jmol
Contents
Protein chains
210 a.a. *
Ligands
PO4 ×2
Metals
_MG ×2
Waters ×402
* Residue conservation analysis
PDB id:
1j97
Name: Hydrolase
Title: Phospho-aspartyl intermediate analogue of phosphoserine phosphatase
Structure: Phosphoserine phosphatase. Chain: a, b. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.50Å     R-factor:   0.189     R-free:   0.209
Authors: H.Cho,W.Wang,R.Kim,H.Yokota,S.Damo,S.-H.Kim,D.Wemmer, S.Kustu,D.Yan,Berkeley Structural Genomics Center (Bsgc)
Key ref:
H.Cho et al. (2001). BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF(3)(-) complex with phosphoserine phosphatase. Proc Natl Acad Sci U S A, 98, 8525-8530. PubMed id: 11438683 DOI: 10.1073/pnas.131213698
Date:
24-May-01     Release date:   25-Jul-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q58989  (SERB_METJA) -  Phosphoserine phosphatase
Seq:
Struc:
211 a.a.
210 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.3  - Phosphoserine phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate
O-phospho-L(or D)-serine
+ H(2)O
= L(or D)-serine
+
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
    Key reference    
 
 
DOI no: 10.1073/pnas.131213698 Proc Natl Acad Sci U S A 98:8525-8530 (2001)
PubMed id: 11438683  
 
 
BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF(3)(-) complex with phosphoserine phosphatase.
H.Cho, W.Wang, R.Kim, H.Yokota, S.Damo, S.H.Kim, D.Wemmer, S.Kustu, D.Yan.
 
  ABSTRACT  
 
Protein phosphoaspartate bonds play a variety of roles. In response regulator proteins of two-component signal transduction systems, phosphorylation of an aspartate residue is coupled to a change from an inactive to an active conformation. In phosphatases and mutases of the haloacid dehalogenase (HAD) superfamily, phosphoaspartate serves as an intermediate in phosphotransfer reactions, and in P-type ATPases, also members of the HAD family, it serves in the conversion of chemical energy to ion gradients. In each case, lability of the phosphoaspartate linkage has hampered a detailed study of the phosphorylated form. For response regulators, this difficulty was recently overcome with a phosphate analog, BeF(3)(-), which yields persistent complexes with the active site aspartate of their receiver domains. We now extend the application of this analog to a HAD superfamily member by solving at 1.5-A resolution the x-ray crystal structure of the complex of BeF(3)(-) with phosphoserine phosphatase (PSP) from Methanococcus jannaschii. The structure is comparable to that of a phosphoenzyme intermediate: BeF(3)(-) is bound to Asp-11 with the tetrahedral geometry of a phosphoryl group, is coordinated to Mg(2+), and is bound to residues surrounding the active site that are conserved in the HAD superfamily. Comparison of the active sites of BeF(3)(-) x PSP and BeF(3)(-) x CeY, a receiver domain/response regulator, reveals striking similarities that provide insights into the function not only of PSP but also of P-type ATPases. Our results indicate that use of BeF(3)(-) for structural studies of proteins that form phosphoaspartate linkages will extend well beyond response regulators.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Ribbon diagram of BeF[ - ]·PSP (A) and stereoview of the active site (B). Ball-and-stick representations of the sidechain carbon, nitrogen, and oxygen atoms are colored green, blue, and red, respectively. In A, the sidechains of highly conserved active site residues, Asp-11, Ser-99, Lys-144, Asp-167, and Asp-171, are shown in ball-and-stick form. BeF[ - ](red balls and orange bonds) is bonded to Asp-11 O in the center of the active site (33). In B, the 2F[o] F[c] electron density map covering the magnesium (cyan) and fluorine (red) atoms was calculated in the absence of these atoms and is shown contoured at 1 . The dashed lines represent hydrogen bonds, salt bridges, and metal-ligand interactions. Three of the Mg2+ ligands (two water molecules and Asp-13-C = O) are not shown.
Figure 4.
Fig. 4. Ribbon diagrams of the Ca^2+-ATPase from rabbit sarcoplasmic reticulum (A) and its catalytic P domain (B) [drawn from coordinates of Toyoshima et al. (32)]. (A) The N (nucleotide-binding), A (actuator), and M (Ca^2+-binding) domains are shown in pink, yellow, and gray, respectively. The latter traverses the membrane of the sarcoplasmic reticulum. The two Ca^2+ ions are shown in red. The catalytic P domain is shown in blue (helices), green ( -strands), and orange (loops). (B) This top-down view was obtained by applying a 90° rotation around the x-axis starting from the orientation in A. The quintet of conserved residues in the P domain is shown in ball-and-stick form in red. Mg2+ was apparently not present in this domain.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21223544 P.Wei, L.C.Milbauer, J.Enenstein, J.Nguyen, W.Pan, and R.P.Hebbel (2011).
Differential endothelial cell gene expression by African Americans versus Caucasian Americans: a possible contribution to health disparity in vascular disease and cancer.
  BMC Med, 9, 2.  
20877901 L.Cipolla, L.Gabrielli, D.Bini, L.Russo, and N.Shaikh (2010).
Kdo: a critical monosaccharide for bacteria viability.
  Nat Prod Rep, 27, 1618-1629.  
20356827 S.Dai, G.A.Murphy, F.Crawford, D.G.Mack, M.T.Falta, P.Marrack, J.W.Kappler, and A.P.Fontenot (2010).
Crystal structure of HLA-DP2 and implications for chronic beryllium disease.
  Proc Natl Acad Sci U S A, 107, 7425-7430.
PDB code: 3lqz
19699748 J.D.Batchelor, H.J.Sterling, E.Hong, E.R.Williams, and D.E.Wemmer (2009).
Receiver domains control the active-state stoichiometry of Aquifex aeolicus sigma54 activator NtrC4, as revealed by electrospray ionization mass spectrometry.
  J Mol Biol, 393, 634-643.  
19726684 T.Biswas, L.Yi, P.Aggarwal, J.Wu, J.R.Rubin, J.A.Stuckey, R.W.Woodard, and O.V.Tsodikov (2009).
The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase.
  J Biol Chem, 284, 30594-30603.
PDB codes: 2r8e 2r8x 2r8y 2r8z 3hyc 3i6b
19364131 Y.Hatori, D.Lewis, C.Toyoshima, and G.Inesi (2009).
Reaction cycle of Thermotoga maritima copper ATPase and conformational characterization of catalytically deficient mutants.
  Biochemistry, 48, 4871-4880.  
19646451 Y.Pazy, A.C.Wollish, S.A.Thomas, P.J.Miller, E.J.Collins, R.B.Bourret, and R.E.Silversmith (2009).
Matching biochemical reaction kinetics to the timescales of life: structural determinants that influence the autodephosphorylation rate of response regulator proteins.
  J Mol Biol, 392, 1205-1220.
PDB codes: 3f7n 3fft 3ffw 3ffx 3fgz
19026779 A.Ghosh, S.Shuman, and C.D.Lima (2008).
The structure of Fcp1, an essential RNA polymerase II CTD phosphatase.
  Mol Cell, 32, 478-490.
PDB codes: 3ef0 3ef1
  18473721 N.K.Bernstein, F.Karimi-Busheri, A.Rasouli-Nia, R.Mani, G.Dianov, J.N.Glover, and M.Weinfeld (2008).
Polynucleotide kinase as a potential target for enhancing cytotoxicity by ionizing radiation and topoisomerase I inhibitors.
  Anticancer Agents Med Chem, 8, 358-367.  
18557815 S.A.Thomas, J.A.Brewster, and R.B.Bourret (2008).
Two variable active site residues modulate response regulator phosphoryl group stability.
  Mol Microbiol, 69, 453-465.  
18562314 Y.Hatori, A.Hirata, C.Toyoshima, D.Lewis, R.Pilankatta, and G.Inesi (2008).
Intermediate phosphorylation reactions in the mechanism of ATP utilization by the copper ATPase (CopA) of Thermotoga maritima.
  J Biol Chem, 283, 22541-22549.  
17493655 H.Zhu, P.Smith, L.K.Wang, and S.Shuman (2007).
Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase.
  Virology, 366, 126-136.
PDB code: 2ia5
17573816 J.S.Fraser, J.P.Merlie, N.Echols, S.R.Weisfield, T.Mignot, D.E.Wemmer, D.R.Zusman, and T.Alber (2007).
An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
  Mol Microbiol, 65, 319-332.
PDB codes: 2gkg 2i6f 2nt3 2nt4
17654724 Q.Xu, K.S.Saikatendu, S.S.Krishna, D.McMullan, P.Abdubek, S.Agarwalla, E.Ambing, T.Astakhova, H.L.Axelrod, D.Carlton, H.J.Chiu, T.Clayton, M.DiDonato, L.Duan, M.A.Elsliger, J.Feuerhelm, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, E.Koesema, M.D.Miller, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, R.Reyes, C.L.Rife, R.Schwarzenbacher, H.van den Bedem, A.White, G.Wolf, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2007).
Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 A resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate.
  Proteins, 69, 433-439.
PDB code: 2fea
17420445 Y.Kim, M.S.Gentry, T.E.Harris, S.E.Wiley, J.C.Lawrence, and J.E.Dixon (2007).
A conserved phosphatase cascade that regulates nuclear membrane biogenesis.
  Proc Natl Acad Sci U S A, 104, 6596-6601.  
16784239 C.Laguri, R.A.Stenzel, T.J.Donohue, M.K.Phillips-Jones, and M.P.Williamson (2006).
Activation of the global gene regulator PrrA (RegA) from Rhodobacter sphaeroides.
  Biochemistry, 45, 7872-7881.  
16582104 D.Strahs, C.X.Zhu, B.Cheng, J.Chen, and Y.C.Tse-Dinh (2006).
Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I.
  Nucleic Acids Res, 34, 1785-1797.  
16628247 E.S.Groban, A.Narayanan, and M.P.Jacobson (2006).
Conformational changes in protein loops and helices induced by post-translational phosphorylation.
  PLoS Comput Biol, 2, e32.  
16990434 N.J.Baxter, L.F.Olguin, M.Golicnik, G.Feng, A.M.Hounslow, W.Bermel, G.M.Blackburn, F.Hollfelder, J.P.Waltho, and N.H.Williams (2006).
A Trojan horse transition state analogue generated by MgF3- formation in an enzyme active site.
  Proc Natl Acad Sci U S A, 103, 14732-14737.  
17070898 S.D.Lahiri, G.Zhang, D.Dunaway-Mariano, and K.N.Allen (2006).
Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage.
  Bioorg Chem, 34, 394-409.
PDB codes: 2iof 2ioh
16882724 S.Y.Park, B.Lowder, A.M.Bilwes, D.F.Blair, and B.R.Crane (2006).
Structure of FliM provides insight into assembly of the switch complex in the bacterial flagella motor.
  Proc Natl Acad Sci U S A, 103, 11886-11891.
PDB code: 2hp7
16983083 Y.A.Chan, M.T.Boyne, A.M.Podevels, A.K.Klimowicz, J.Handelsman, N.L.Kelleher, and M.G.Thomas (2006).
Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units.
  Proc Natl Acad Sci U S A, 103, 14349-14354.  
16322582 A.Toro-Roman, T.Wu, and A.M.Stock (2005).
A common dimerization interface in bacterial response regulators KdpE and TorR.
  Protein Sci, 14, 3077-3088.
PDB codes: 1zgz 1zh2 1zh4
16269752 P.Peters-Wendisch, M.Stolz, H.Etterich, N.Kennerknecht, H.Sahm, and L.Eggeling (2005).
Metabolic engineering of Corynebacterium glutamicum for L-serine production.
  Appl Environ Microbiol, 71, 7139-7144.  
15183870 A.M.Ahmed, and T.Shimamoto (2004).
A plasmid-encoded class 1 integron carrying sat, a putative phosphoserine phosphatase gene and aadA2 from enterotoxigenic Escherichia coli O159 isolated in Japan.
  FEMS Microbiol Lett, 235, 243-248.  
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
15291819 Y.Peeraer, A.Rabijns, J.F.Collet, E.Van Schaftingen, and C.De Ranter (2004).
How calcium inhibits the magnesium-dependent enzyme human phosphoserine phosphatase.
  Eur J Biochem, 271, 3421-3427.  
12824492 D.H.Shin, A.Roberts, J.Jancarik, H.Yokota, R.Kim, D.E.Wemmer, and S.H.Kim (2003).
Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima.
  Protein Sci, 12, 1464-1472.
PDB code: 1nf2
12777814 L.Chooback, and A.H.West (2003).
Co-crystallization of the yeast phosphorelay protein YPD1 with the SLN1 response-regulator domain and preliminary X-ray diffraction analysis.
  Acta Crystallogr D Biol Crystallogr, 59, 927-929.  
14628053 T.L.Tootle, S.J.Silver, E.L.Davies, V.Newman, R.R.Latek, I.A.Mills, J.D.Selengut, B.E.Parlikar, and I.Rebay (2003).
The transcription factor Eyes absent is a protein tyrosine phosphatase.
  Nature, 426, 299-302.  
12777757 Y.Peeraer, A.Rabijns, C.Verboven, J.F.Collet, E.Van Schaftingen, and C.De Ranter (2003).
High-resolution structure of human phosphoserine phosphatase in open conformation.
  Acta Crystallogr D Biol Crystallogr, 59, 971-977.
PDB code: 1nnl
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
12220496 E.A.Galburt, J.Pelletier, G.Wilson, and B.L.Stoddard (2002).
Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase.
  Structure, 10, 1249-1260.
PDB code: 1ltq
11842120 L.K.Wang, and S.Shuman (2002).
Mutational analysis defines the 5'-kinase and 3'-phosphatase active sites of T4 polynucleotide kinase.
  Nucleic Acids Res, 30, 1073-1080.  
11741839 R.B.Bourret, N.W.Charon, A.M.Stock, and A.H.West (2002).
Bright lights, abundant operons--fluorescence and genomic technologies advance studies of bacterial locomotion and signal transduction: review of the BLAST meeting, Cuernavaca, Mexico, 14 to 19 January 2001.
  J Bacteriol, 184, 1.  
12081483 S.D.Lahiri, G.Zhang, D.Dunaway-Mariano, and K.N.Allen (2002).
Caught in the act: the structure of phosphorylated beta-phosphoglucomutase from Lactococcus lactis.
  Biochemistry, 41, 8351-8359.
PDB code: 1lvh
11459948 P.R.Thompson, and P.A.Cole (2001).
Probing the mechanism of enzymatic phosphoryl transfer with a chemical trick.
  Proc Natl Acad Sci U S A, 98, 8170-8171.  
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 code is shown on the right.