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Viral protein, hydrolase PDB id
1g5b
Jmol
Contents
Protein chains
219 a.a. *
Ligands
SO4 ×4
Metals
_MN ×6
_HG ×2
Waters ×305
* Residue conservation analysis
PDB id:
1g5b
Name: Viral protein, hydrolase
Title: Bacteriophage lambda ser/thr protein phosphatase
Structure: Serine/threonine protein phosphatase. Chain: a, b, c. Engineered: yes
Source: Enterobacteria phage lambda. Organism_taxid: 10710. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.15Å     R-factor:   0.200     R-free:   0.226
Authors: W.C.Voegtli,D.J.White,N.J.Reiter,F.Rusnak,A.C.Rosenzweig
Key ref:
W.C.Voegtli et al. (2000). Structure of the bacteriophage lambda Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes. Biochemistry, 39, 15365-15374. PubMed id: 11112522 DOI: 10.1021/bi0021030
Date:
31-Oct-00     Release date:   07-Mar-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03772  (PP_LAMBD) -  Serine/threonine-protein phosphatase
Seq:
Struc: 		221 a.a.
219 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.3.1.3.16  - Phosphoprotein phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphoprotein + H2O = a protein + phosphate
phosphoprotein
 + H(2)O
 = protein
 + phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     hydrolase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi0021030 Biochemistry 39:15365-15374 (2000)
PubMed id: 11112522  
 
 
Structure of the bacteriophage lambda Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes.
W.C.Voegtli, D.J.White, N.J.Reiter, F.Rusnak, A.C.Rosenzweig.
 
  ABSTRACT  
 
The protein phosphatase encoded by bacteriophage lambda (lambda PP) belongs to a family of Ser/Thr phosphatases (Ser/Thr PPases) that includes the eukaryotic protein phosphatases 1 (PP1), 2A (PP2A), and 2B (calcineurin). These Ser/Thr PPases and the related purple acid phosphatases (PAPs) contain a conserved phosphoesterase sequence motif that binds a dinuclear metal center. The mechanisms of phosphoester hydrolysis by these enzymes are beginning to be unraveled. To utilize lambda PP more effectively as a model for probing the catalytic mechanism of the Ser/Thr PPases, we have determined its crystal structure to 2.15 A resolution. The overall fold resembles that of PP1 and calcineurin, including a conserved beta alpha beta alpha beta structure that comprises the phosphoesterase motif. Substrates and inhibitors probably bind in a narrow surface groove that houses the active site dinuclear Mn(II) center. The arrangement of metal ligands is similar to that in PP1, calcineurin, and PAP, and a bound sulfate ion is present in two novel coordination modes. In two of the three molecules in the crystallographic asymmetric unit, sulfate is coordinated to Mn2 in a monodentate, terminal fashion, and the two Mn(II) ions are bridged by a solvent molecule. Two additional solvent molecules are coordinated to Mn1. In the third molecule, the sulfate ion is triply coordinated to the metal center with one oxygen coordinated to both Mn(II) ions, one oxygen coordinated to Mn1, and one oxygen coordinated to Mn2. The sulfate in this coordination mode displaces the bridging ligand and one of the terminal solvent ligands. In both sulfate coordination modes, the sulfate ion is stabilized by hydrogen bonding interactions with conserved arginine residues, Arg 53 and Arg 162. The two different active site structures provide models for intermediates in phosphoester hydrolysis and suggest specific mechanistic roles for conserved residues.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
19801656 M.Podobnik, R.Tyagi, N.Matange, U.Dermol, A.K.Gupta, R.Mattoo, K.Seshadri, and S.S.Visweswariah (2009).
A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability.
  J Biol Chem, 284, 32846-32857.
PDB codes: 3ib7 3ib8
19706604 R.García-Hernández, A.Moraleda-Muñoz, A.Castañeda-García, J.Pérez, and J.Muñoz-Dorado (2009).
Myxococcus xanthus Pph2 is a manganese-dependent protein phosphatase involved in energy metabolism.
  J Biol Chem, 284, 28720-28728.  
19004815 R.Tyagi, A.R.Shenoy, and S.S.Visweswariah (2009).
Characterization of an Evolutionarily Conserved Metallophosphoesterase That Is Expressed in the Fetal Brain and Associated with the WAGR Syndrome.
  J Biol Chem, 284, 5217-5228.  
18234116 G.Schenk, T.W.Elliott, E.Leung, L.E.Carrington, N.Mitić, L.R.Gahan, and L.W.Guddat (2008).
Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle.
  BMC Struct Biol, 8, 6.
PDB codes: 2qfp 2qfr
18771593 K.S.Hadler, T.Huber, A.I.Cassady, J.Weber, J.Robinson, A.Burrows, G.Kelly, L.W.Guddat, D.A.Hume, G.Schenk, and J.U.Flanagan (2008).
Identification of a non-purple tartrate-resistant acid phosphatase: an evolutionary link to Ser/Thr protein phosphatases?
  BMC Res Notes, 1, 78.  
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.  
17986465 N.Keppetipola, and S.Shuman (2007).
Characterization of the 2',3' cyclic phosphodiesterase activities of Clostridium thermocellum polynucleotide kinase-phosphatase and bacteriophage lambda phosphatase.
  Nucleic Acids Res, 35, 7721-7732.  
16540477 H.Zhu, and S.Shuman (2006).
Substrate specificity and structure-function analysis of the 3'-phosphoesterase component of the bacterial NHEJ protein, DNA ligase D.
  J Biol Chem, 281, 13873-13881.  
16301605 N.Keppetipola, and S.Shuman (2006).
Mechanism of the phosphatase component of Clostridium thermocellum polynucleotide kinase-phosphatase.
  RNA, 12, 73-82.  
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.  
17006950 Q.H.Wang, W.X.Hu, W.Gao, and R.C.Bi (2006).
Crystal structure of the diadenosine tetraphosphate hydrolase from Shigella flexneri 2a.
  Proteins, 65, 1032-1035.
PDB code: 2dfj
15987807 A.Martins, and S.Shuman (2005).
An end-healing enzyme from Clostridium thermocellum with 5' kinase, 2',3' phosphatase, and adenylyltransferase activities.
  RNA, 11, 1271-1280.  
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.  
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
16096803 E.G.Funhoff, T.E.de Jongh, and B.A.Averill (2005).
Direct observation of multiple protonation states in recombinant human purple acid phosphatase.
  J Biol Inorg Chem, 10, 550-563.  
15955057 E.G.Funhoff, Y.Wang, G.Andersson, and B.A.Averill (2005).
Substrate positioning by His92 is important in catalysis by purple acid phosphatase.
  FEBS J, 272, 2968-2977.  
15625111 G.Schenk, L.R.Gahan, L.E.Carrington, N.Mitic, M.Valizadeh, S.E.Hamilton, J.de Jersey, and L.W.Guddat (2005).
Phosphate forms an unusual tripodal complex with the Fe-Mn center of sweet potato purple acid phosphatase.
  Proc Natl Acad Sci U S A, 102, 273-278.
PDB code: 1xzw
16275784 M.F.Khalid, M.J.Damha, S.Shuman, and B.Schwer (2005).
Structure-function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase.
  Nucleic Acids Res, 33, 6349-6360.  
15956667 S.Hayes, K.Asai, A.M.Chu, and C.Hayes (2005).
NinR- and red-mediated phage-prophage marker rescue recombination in Escherichia coli: recovery of a nonhomologous immlambda DNA segment by infecting lambdaimm434 phages.
  Genetics, 170, 1485-1499.  
15555063 A.V.Andreeva, and M.A.Kutuzov (2004).
Widespread presence of "bacterial-like" PPP phosphatases in eukaryotes.
  BMC Evol Biol, 4, 47.  
14981312 H.Tsuruta, J.Tamura, H.Yamagata, and Y.Aizono (2004).
Specification of amino acid residues essential for the catalytic reaction of cold-active protein-tyrosine phosphatase of a psychrophile, Shewanella sp.
  Biosci Biotechnol Biochem, 68, 440-443.  
15489417 M.B.Łobocka, D.J.Rose, G.Plunkett, M.Rusin, A.Samojedny, H.Lehnherr, M.B.Yarmolinsky, and F.R.Blattner (2004).
Genome of bacteriophage P1.
  J Bacteriol, 186, 7032-7068.  
15155720 M.R.Swingle, R.E.Honkanen, and E.M.Ciszak (2004).
Structural basis for the catalytic activity of human serine/threonine protein phosphatase-5.
  J Biol Chem, 279, 33992-33999.
PDB code: 1s95
15381847 S.Barik (2004).
When proteome meets genome: the alpha helix and the beta strand of proteins are eschewed by mRNA splice junctions and may define the minimal indivisible modules of protein architecture.
  J Biosci, 29, 261-273.  
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
14529289 O.Schilling, N.Wenzel, M.Naylor, A.Vogel, M.Crowder, C.Makaroff, and W.Meyer-Klaucke (2003).
Flexible metal binding of the metallo-beta-lactamase domain: glyoxalase II incorporates iron, manganese, and zinc in vivo.
  Biochemistry, 42, 11777-11786.  
11717262 L.Shi, D.G.Kehres, and M.E.Maguire (2001).
The PPP-family protein phosphatases PrpA and PrpB of Salmonella enterica serovar Typhimurium possess distinct biochemical properties.
  J Bacteriol, 183, 7053-7057.  
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.