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PDBsum entry 1f5s

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1f5s
Jmol
Contents
Protein chains
210 a.a. *
Ligands
PO4 ×4
Metals
_MG ×2
Waters ×383
* Residue conservation analysis
PDB id:
1f5s
Name: Hydrolase
Title: Crystal structure of phosphoserine phosphatase from methanococcus jannaschii
Structure: Phosphoserine phosphatase (psp). Chain: a, b. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Strain: mj1594. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.80Å     R-factor:   0.198     R-free:   0.235
Authors: W.Wang,R.Kim,J.Jancarik,H.Yokota,S.H.Kim,Berkeley Structural Genomics Center (Bsgc)
Key ref:
W.Wang et al. (2001). Crystal structure of phosphoserine phosphatase from Methanococcus jannaschii, a hyperthermophile, at 1.8 A resolution. Structure, 9, 65-71. PubMed id: 11342136 DOI: 10.1016/S0969-2126(00)00558-X
Date:
15-Jun-00     Release date:   20-Jun-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

 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: 10.1016/S0969-2126(00)00558-X Structure 9:65-71 (2001)
PubMed id: 11342136  
 
 
Crystal structure of phosphoserine phosphatase from Methanococcus jannaschii, a hyperthermophile, at 1.8 A resolution.
W.Wang, R.Kim, J.Jancarik, H.Yokota, S.H.Kim.
 
  ABSTRACT  
 
BACKGROUND: D-Serine is a co-agonist of the N-methyl-D-aspartate subtype of glutamate receptors, a major neurotransmitter receptor family in mammalian nervous systems. D-Serine is converted from L-serine, 90% of which is the product of the enzyme phosphoserine phosphatase (PSP). PSP from M. jannaschii (MJ) shares significant sequence homology with human PSP. PSPs and P-type ATPases are members of the haloacid dehalogenase (HAD)-like hydrolase family, and all members share three conserved sequence motifs. PSP and P-type ATPases utilize a common mechanism that involves Mg(2+)-dependent phosphorylation and autodephosphorylation at an aspartyl side chain in the active site. The strong resemblance in sequence and mechanism implies structural similarity among these enzymes. RESULTS: The PSP crystal structure resembles the NAD(P) binding Rossmann fold with a large insertion of a four-helix-bundle domain and a beta hairpin. Three known conserved sequence motifs are arranged next to each other in space and outline the active site. A phosphate and a magnesium ion are bound to the active site. The active site is within a closed environment between the core alpha/beta domain and the four-helix-bundle domain. CONCLUSIONS: The crystal structure of MJ PSP was determined at 1.8 A resolution. Critical residues were assigned based on the active site structure and ligand binding geometry. The PSP structure is in a closed conformation that may resemble the phosphoserine bound state or the state after autodephosphorylation. Compared to a P-type ATPase (Ca(2+)-ATPase) structure, which is in an open state, this PSP structure appears also to be a good model for the closed conformation of P-type ATPase.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Ribbon Diagram of PSP Structure and Hydrogen Bond Network of Its Active Site(a) Stereo view of the PSP structure presented in a ribbon diagram. The three conserved motifs are colored in red. The orange molecule depicts the phosphate in the active site. The green ball depicts the Mg2+ ion.(b) A schematic plot of the hydrogen bond network in the active site. All the H bonds that involve the ligands, and part of the H-bonds that do not involve the ligands, are shown as dotted lines. The unit for the distances is in . The Mg2+ achieves the hexavalent coordination through interactions with the phosphate, Asp-11, Asp-13, Asp-167, and water molecules W222 and W223. W222 and W223, in turn, interact with the surrounding residues including Asp-167, Glu-20, Asp-171, Asp-170, and the phosphate. Asp-11 adopts discrete sidechain conformations 1 and 2. Both conformations coordinate with the Mg2+. Conformer 1 also interacts with the phosphate while conformer 2 is remote form the phosphate but forms an H bond with the Thr-15 sidechain. The phosphate forms H bonds with residues from all three motifs. The H bond between O1 and Asp-11 suggests that either O1 or Asp-11 is protonated.
 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 65-71) copyright 2001.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21396942 K.Walldén, and P.Nordlund (2011).
Structural Basis for the Allosteric Regulation and Substrate Recognition of Human Cytosolic 5'-Nucleotidase II.
  J Mol Biol, 408, 684-696.
PDB codes: 2xcv 2xcw 2xcx 2xjb 2xjc 2xjd 2xje 2xjf
20652880 S.Re, T.Imai, J.Jung, S.Ten-No, and Y.Sugita (2011).
Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation.
  J Comput Chem, 32, 260-270.  
20050614 H.H.Nguyen, L.Wang, H.Huang, E.Peisach, D.Dunaway-Mariano, and K.N.Allen (2010).
Structural determinants of substrate recognition in the HAD superfamily member D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) .
  Biochemistry, 49, 1082-1092.
PDB codes: 3l8e 3l8f 3l8g 3l8h
20809990 J.V.Møller, C.Olesen, A.M.Winther, and P.Nissen (2010).
The sarcoplasmic Ca2+-ATPase: design of a perfect chemi-osmotic pump.
  Q Rev Biophys, 43, 501-566.  
20877901 L.Cipolla, L.Gabrielli, D.Bini, L.Russo, and N.Shaikh (2010).
Kdo: a critical monosaccharide for bacteria viability.
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20135339 L.H.Otero, P.R.Beassoni, A.T.Lisa, and C.E.Domenech (2010).
Transition from octahedral to tetrahedral geometry causes the activation or inhibition by Znf2+ of Pseudomonas aeruginosa phosphorylcholine phosphatase.
  Biometals, 23, 307-314.  
20551224 W.Yang, M.Pollard, Y.Li-Beisson, F.Beisson, M.Feig, and J.Ohlrogge (2010).
A distinct type of glycerol-3-phosphate acyltransferase with sn-2 preference and phosphatase activity producing 2-monoacylglycerol.
  Proc Natl Acad Sci U S A, 107, 12040-12045.  
19122187 A.A.Badejo, H.A.Eltelib, K.Fukunaga, Y.Fujikawa, and M.Esaka (2009).
Increase in ascorbate content of transgenic tobacco plants overexpressing the acerola (Malpighia glabra) phosphomannomutase gene.
  Plant Cell Physiol, 50, 423-428.  
19168029 L.Cao, P.Zhang, and D.F.Grant (2009).
An insect farnesyl phosphatase homologous to the N-terminal domain of soluble epoxide hydrolase.
  Biochem Biophys Res Commun, 380, 188-192.  
19340413 M.Decker, M.Arand, and A.Cronin (2009).
Mammalian epoxide hydrolases in xenobiotic metabolism and signalling.
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19879837 Y.Shi (2009).
Serine/threonine phosphatases: mechanism through structure.
  Cell, 139, 468-484.  
18045868 A.R.Diaz, S.Stephenson, J.M.Green, V.M.Levdikov, A.J.Wilkinson, and M.Perego (2008).
Functional Role for a Conserved Aspartate in the Spo0E Signature Motif Involved in the Dephosphorylation of the Bacillus subtilis Sporulation Regulator Spo0A.
  J Biol Chem, 283, 2962-2972.  
18931414 H.Yamamoto, K.Takio, M.Sugahara, and N.Kunishima (2008).
Structure of a haloacid dehalogenase superfamily phosphatase PH1421 from Pyrococcus horikoshii OT3: oligomeric state and thermoadaptation mechanism.
  Acta Crystallogr D Biol Crystallogr, 64, 1068-1077.
PDB code: 1wr8
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.  
19018103 T.Kawamura, N.Watanabe, and I.Tanaka (2008).
Structure of mannosyl-3-phosphoglycerate phosphatase from Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 64, 1267-1276.
PDB codes: 1wzc 2zos
18256491 Y.Nagahashi, M.Tazoe, and T.Hoshino (2008).
Cloning of the pyridoxine 5'-phosphate phosphatase gene (pdxP) and vitamin B6 production in pdxP recombinant Sinorhizobium meliloti.
  Biosci Biotechnol Biochem, 72, 421-427.  
17405878 K.Walldén, P.Stenmark, T.Nyman, S.Flodin, S.Gräslund, P.Loppnau, V.Bianchi, and P.Nordlund (2007).
Crystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition.
  J Biol Chem, 282, 17828-17836.
PDB codes: 2cn1 2j2c 2jc9 2jcm 2jga
18058037 S.C.Almo, J.B.Bonanno, J.M.Sauder, S.Emtage, T.P.Dilorenzo, V.Malashkevich, S.R.Wasserman, S.Swaminathan, S.Eswaramoorthy, R.Agarwal, D.Kumaran, M.Madegowda, S.Ragumani, Y.Patskovsky, J.Alvarado, U.A.Ramagopal, J.Faber-Barata, M.R.Chance, A.Sali, A.Fiser, Z.Y.Zhang, D.S.Lawrence, and S.K.Burley (2007).
Structural genomics of protein phosphatases.
  J Struct Funct Genomics, 8, 121-140.
PDB codes: 1rxd 2fh7 2g59 2hcm 2hhl 2hxp 2hy3 2i0o 2i1y 2i44 2iq1 2irm 2isn 2nv5 2oyc 2p27 2p4u 2p69 2p8e 2pbn 2q5e 2qjc 2r0b
16672222 E.Bitto, C.A.Bingman, G.E.Wesenberg, J.G.McCoy, and G.N.Phillips (2006).
Structure of pyrimidine 5'-nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning.
  J Biol Chem, 281, 20521-20529.
PDB codes: 2bdu 2g06 2g07 2g08 2g09 2g0a
16990279 E.Kuznetsova, M.Proudfoot, C.F.Gonzalez, G.Brown, M.V.Omelchenko, I.Borozan, L.Carmel, Y.I.Wolf, H.Mori, A.V.Savchenko, C.H.Arrowsmith, E.V.Koonin, A.M.Edwards, and A.F.Yakunin (2006).
Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family.
  J Biol Chem, 281, 36149-36161.  
16966333 E.S.Rangarajan, A.Proteau, J.Wagner, M.N.Hung, A.Matte, and M.Cygler (2006).
Structural snapshots of Escherichia coli histidinol phosphate phosphatase along the reaction pathway.
  J Biol Chem, 281, 37930-37941.
PDB codes: 2fpr 2fps 2fpu 2fpw 2fpx
16815921 K.N.Rao, D.Kumaran, J.Seetharaman, J.B.Bonanno, S.K.Burley, and S.Swaminathan (2006).
Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications.
  Protein Sci, 15, 1735-1744.
PDB code: 1u02
17106798 P.R.Beassoni, L.H.Otero, M.J.Massimelli, A.T.Lisa, and C.E.Domenech (2006).
Critical active-site residues identified by site-directed mutagenesis in Pseudomonas aeruginosa phosphorylcholine phosphatase, a new member of the haloacid dehalogenases hydrolase superfamily.
  Curr Microbiol, 53, 534-539.  
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
15591322 A.K.Nagy, D.J.Kane, C.M.Tran, R.A.Farley, and L.D.Faller (2005).
Evidence calcium pump binds magnesium before inorganic phosphate.
  J Biol Chem, 280, 7435-7443.  
15657928 A.Roberts, S.Y.Lee, E.McCullagh, R.E.Silversmith, and D.E.Wemmer (2005).
YbiV from Escherichia coli K12 is a HAD phosphatase.
  Proteins, 58, 790-801.
PDB codes: 1rlm 1rlo 1rlt
  16511085 H.Wang, H.Pang, Y.Ding, Y.Li, X.Wu, and Z.Rao (2005).
Purification, crystallization and preliminary X-ray diffraction analysis of human enolase-phosphatase E1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 521-523.  
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.  
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.  
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.  
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.  
15606776 S.Allegrini, A.Scaloni, M.G.Careddu, G.Cuccu, C.D'Ambrosio, R.Pesi, M.Camici, L.Ferrara, and M.G.Tozzi (2004).
Mechanistic studies on bovine cytosolic 5'-nucleotidase II, an enzyme belonging to the HAD superfamily.
  Eur J Biochem, 271, 4881-4891.  
14699121 S.K.Singh, K.Yang, S.Karthikeyan, T.Huynh, X.Zhang, M.A.Phillips, and H.Zhang (2004).
The thrH gene product of Pseudomonas aeruginosa is a dual activity enzyme with a novel phosphoserine:homoserine phosphotransferase activity.
  J Biol Chem, 279, 13166-13173.
PDB codes: 1rku 1rkv
14555659 Y.Kim, A.F.Yakunin, E.Kuznetsova, X.Xu, M.Pennycooke, J.Gu, F.Cheung, M.Proudfoot, C.H.Arrowsmith, A.Joachimiak, A.M.Edwards, and D.Christendat (2004).
Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum.
  J Biol Chem, 279, 517-526.
PDB code: 1l6r
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.  
12777773 C.Forleo, M.Benvenuti, V.Calderone, S.Schippa, J.D.Docquier, M.C.Thaller, G.M.Rossolini, and S.Mangani (2003).
Expression, purification, crystallization and preliminary X-ray characterization of the class B acid phosphatase (AphA) from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 59, 1058-1060.  
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
12639950 J.Wu, and R.W.Woodard (2003).
Escherichia coli YrbI is 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase.
  J Biol Chem, 278, 18117-18123.  
  12763820 L.D.Faller, A.K.Nagy, D.J.Kane, and R.A.Farley (2003).
Mechanism of phosphoryl group transfer.
  Ann N Y Acad Sci, 986, 275-277.  
12975374 L.Dode, J.P.Andersen, N.Leslie, J.Dhitavat, B.Vilsen, and A.Hovnanian (2003).
Dissection of the functional differences between sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) 1 and 2 isoforms and characterization of Darier disease (SERCA2) mutants by steady-state and transient kinetic analyses.
  J Biol Chem, 278, 47877-47889.  
  12763773 S.J.Karlish (2003).
Investigating the energy transduction mechanism of P-type ATPases with Fe2+-catalyzed oxidative cleavage.
  Ann N Y Acad Sci, 986, 39-49.  
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
12213811 H.Y.Kim, Y.S.Heo, J.H.Kim, M.H.Park, J.Moon, E.Kim, D.Kwon, J.Yoon, D.Shin, E.J.Jeong, S.Y.Park, T.G.Lee, Y.H.Jeon, S.Ro, J.M.Cho, and K.Y.Hwang (2002).
Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase.
  J Biol Chem, 277, 46651-46658.
PDB codes: 1l8l 1l8o
11835514 J.F.Parsons, K.Lim, A.Tempczyk, W.Krajewski, E.Eisenstein, and O.Herzberg (2002).
From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase.
  Proteins, 46, 393-404.
PDB codes: 1j8d 1k1e
12392557 O.Radresa, K.Ogata, S.Wodak, J.M.Ruysschaert, and E.Goormaghtigh (2002).
Modeling the three-dimensional structure of H+-ATPase of Neurospora crassa.
  Eur J Biochem, 269, 5246-5258.  
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
11438683 H.Cho, W.Wang, R.Kim, H.Yokota, S.Damo, S.H.Kim, D.Wemmer, S.Kustu, and D.Yan (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.
PDB code: 1j97
11406387 S.A.Teichmann, A.G.Murzin, and C.Chothia (2001).
Determination of protein function, evolution and interactions by structural genomics.
  Curr Opin Struct Biol, 11, 354-363.  
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.