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PDBsum entry 1ohe

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Hydrolase PDB id
1ohe
Jmol
Contents
Protein chain
339 a.a. *
Ligands
ACE-ALA-SEP-PRO
Waters ×143
* Residue conservation analysis
PDB id:
1ohe
Name: Hydrolase
Title: Structure of cdc14b phosphatase with a peptide ligand
Structure: Cdc14b2 phosphatase. Chain: a. Fragment: core domain, residues 39-386. Synonym: cdc14b. Engineered: yes. Peptide ligand. Chain: b. Other_details: substrate
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: baculovirus/insect cell. Synthetic: non-biological sequence. Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.207     R-free:   0.253
Authors: C.H.Gray,V.M.Good,N.K.Tonks,D.Barford
Key ref: C.H.Gray et al. (2003). The structure of the cell cycle protein Cdc14 reveals a proline-directed protein phosphatase. EMBO J, 22, 3524-3535. PubMed id: 12853468
Date:
24-May-03     Release date:   24-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O60729  (CC14B_HUMAN) -  Dual specificity protein phosphatase CDC14B
Seq:
Struc:
498 a.a.
339 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.3.1.3.16  - Protein-serine/threonine phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: [a protein]-serine/threonine phosphate + H2O = [a protein]- serine/threonine + phosphate
[a protein]-serine/threonine phosphate
+ H(2)O
= [a protein]- serine/threonine
+
phosphate
Bound ligand (Het Group name = SEP)
matches with 50.00% similarity
   Enzyme class 2: E.C.3.1.3.48  - Protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate
Protein tyrosine phosphate
+ H(2)O
= protein tyrosine
+
phosphate
Bound ligand (Het Group name = SEP)
matches with 50.00% similarity
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     dephosphorylation   3 terms 
  Biochemical function     phosphatase activity     3 terms  

 

 
    reference    
 
 
EMBO J 22:3524-3535 (2003)
PubMed id: 12853468  
 
 
The structure of the cell cycle protein Cdc14 reveals a proline-directed protein phosphatase.
C.H.Gray, V.M.Good, N.K.Tonks, D.Barford.
 
  ABSTRACT  
 
The Cdc14 family of dual-specificity protein phosphatases (DSPs) is conserved within eukaryotes and functions to down-regulate mitotic Cdk activities, promoting cytokinesis and mitotic exit. We have integrated structural and kinetic analyses to define the molecular mechanism of the dephosphorylation reaction catalysed by Cdc14. The structure of Cdc14 illustrates a novel arrangement of two domains, each with a DSP-like fold, arranged in tandem. The C-terminal domain contains the conserved PTP motif of the catalytic site, whereas the N-terminal domain, which shares no sequence similarity with other DSPs, contributes to substrate specificity, and lacks catalytic activity. The catalytic site is located at the base of a pronounced surface channel formed by the interface of the two domains, and regions of both domains interact with the phosphopeptide substrate. Specificity for a pSer-Pro motif is mediated by a hydrophobic pocket that is capable of accommodating the apolar Pro(P+1) residue of the peptide. Our structural and kinetic data support a role for Cdc14 in the preferential dephosphorylation of proteins modified by proline-directed kinases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21379580 I.Tumurbaatar, O.Cizmecioglu, I.Hoffmann, I.Grummt, and R.Voit (2011).
Human Cdc14B promotes progression through mitosis by dephosphorylating Cdc25 and regulating Cdk1/cyclin B activity.
  PLoS One, 6, e14711.  
21549314 N.A.Lyons, and D.O.Morgan (2011).
Cdk1-dependent destruction of eco1 prevents cohesion establishment after s phase.
  Mol Cell, 42, 378-389.  
20956543 M.D.Vázquez-Novelle, N.Mailand, S.Ovejero, A.Bueno, and M.P.Sacristán (2010).
Human Cdc14A phosphatase modulates the G2/M transition through Cdc25A and Cdc25B.
  J Biol Chem, 285, 40544-40553.  
20236090 P.L.Tanguay, G.Rodier, and S.Meloche (2010).
C-terminal domain phosphorylation of ERK3 controlled by Cdk1 and Cdc14 regulates its stability in mitosis.
  Biochem J, 428, 103-111.  
20603077 R.H.Roberts-Galbraith, M.D.Ohi, B.A.Ballif, J.S.Chen, I.McLeod, W.H.McDonald, S.P.Gygi, J.R.Yates, and K.L.Gould (2010).
Dephosphorylation of F-BAR protein Cdc15 modulates its conformation and stimulates its scaffolding activity at the cell division site.
  Mol Cell, 39, 86-99.  
19489729 A.Edwards (2009).
Large-scale structural biology of the human proteome.
  Annu Rev Biochem, 78, 541-568.  
18433060 D.J.Aceti, E.Bitto, A.F.Yakunin, M.Proudfoot, C.A.Bingman, R.O.Frederick, H.K.Sreenath, F.C.Vojtik, R.L.Wrobel, B.G.Fox, J.L.Markley, and G.N.Phillips (2008).
Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000.
  Proteins, 73, 241-253.
PDB code: 1xri
18845678 F.Jin, H.Liu, F.Liang, R.Rizkallah, M.M.Hurt, and Y.Wang (2008).
Temporal control of the dephosphorylation of Cdk substrates by mitotic exit pathways in budding yeast.
  Proc Natl Acad Sci U S A, 105, 16177-16182.  
18239684 G.Rodier, P.Coulombe, P.L.Tanguay, C.Boutonnet, and S.Meloche (2008).
Phosphorylation of Skp2 regulated by CDK2 and Cdc14B protects it from degradation by APC(Cdh1) in G1 phase.
  EMBO J, 27, 679-691.  
18547142 L.Rosso, A.C.Marques, M.Weier, N.Lambert, M.A.Lambot, P.Vanderhaeghen, and H.Kaessmann (2008).
Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein.
  PLoS Biol, 6, e140.  
18287090 M.C.Hall, D.E.Jeong, J.T.Henderson, E.Choi, S.C.Bremmer, A.B.Iliuk, and H.Charbonneau (2008).
Cdc28 and Cdc14 control stability of the anaphase-promoting complex inhibitor Acm1.
  J Biol Chem, 283, 10396-10407.  
18298792 R.Pulido, and R.Hooft van Huijsduijnen (2008).
Protein tyrosine phosphatases: dual-specificity phosphatases in health and disease.
  FEBS J, 275, 848-866.  
17173287 H.M.Chu, and A.H.Wang (2007).
Enzyme-substrate interactions revealed by the crystal structures of the archaeal Sulfolobus PTP-fold phosphatase and its phosphopeptide complexes.
  Proteins, 66, 996.
PDB codes: 2dxp 2i6i 2i6j 2i6m 2i6o 2i6p
17347519 H.O.Park, and E.Bi (2007).
Central roles of small GTPases in the development of cell polarity in yeast and beyond.
  Microbiol Mol Biol Rev, 71, 48-96.  
17585314 J.A.Ubersax, and J.E.Ferrell (2007).
Mechanisms of specificity in protein phosphorylation.
  Nat Rev Mol Cell Biol, 8, 530-541.  
17116692 J.Bloom, and F.R.Cross (2007).
Novel role for Cdc14 sequestration: Cdc14 dephosphorylates factors that promote DNA replication.
  Mol Cell Biol, 27, 842-853.  
17349956 L.J.Holt, J.E.Hutti, L.C.Cantley, and D.O.Morgan (2007).
Evolution of Ime2 phosphorylation sites on Cdk1 substrates provides a mechanism to limit the effects of the phosphatase Cdc14 in meiosis.
  Mol Cell, 25, 689-702.  
17371873 L.Lanzetti, V.Margaria, F.Melander, L.Virgili, M.H.Lee, J.Bartek, and S.Jensen (2007).
Regulation of the Rab5 GTPase-activating protein RN-tre by the dual specificity phosphatase Cdc14A in human cells.
  J Biol Chem, 282, 15258-15270.  
17427953 S.K.Jung, D.G.Jeong, T.S.Yoon, J.H.Kim, S.E.Ryu, and S.J.Kim (2007).
Crystal structure of human slingshot phosphatase 2.
  Proteins, 68, 408-412.
PDB code: 2nt2
16449187 R.Fraschini, C.D'Ambrosio, M.Venturetti, G.Lucchini, and S.Piatti (2006).
Disappearance of the budding yeast Bub2-Bfa1 complex from the mother-bound spindle pole contributes to mitotic exit.
  J Cell Biol, 172, 335-346.  
15713658 A.Changela, A.Martins, S.Shuman, and A.Mondragón (2005).
Crystal structure of baculovirus RNA triphosphatase complexed with phosphate.
  J Biol Chem, 280, 17848-17856.
PDB code: 1yn9
15653073 B.A.Wolfe, and K.L.Gould (2005).
Split decisions: coordinating cytokinesis in yeast.
  Trends Cell Biol, 15, 10-18.  
16027160 C.Slawson, N.E.Zachara, K.Vosseller, W.D.Cheung, M.D.Lane, and G.W.Hart (2005).
Perturbations in O-linked beta-N-acetylglucosamine protein modification cause severe defects in mitotic progression and cytokinesis.
  J Biol Chem, 280, 32944-32956.  
15800637 F.V.Rivas, N.H.Tolia, J.J.Song, J.P.Aragon, J.Liu, G.J.Hannon, and L.Joshua-Tor (2005).
Purified Argonaute2 and an siRNA form recombinant human RISC.
  Nat Struct Mol Biol, 12, 340-349.
PDB codes: 1z25 1z26
15899858 H.P.Cho, Y.Liu, M.Gomez, J.Dunlap, M.Tyers, and Y.Wang (2005).
The dual-specificity phosphatase CDC14B bundles and stabilizes microtubules.
  Mol Cell Biol, 25, 4541-4551.  
16176976 J.Stoepel, M.A.Ottey, C.Kurischko, P.Hieter, and F.C.Luca (2005).
The mitotic exit network Mob1p-Dbf2p kinase complex localizes to the nucleus and regulates passenger protein localization.
  Mol Biol Cell, 16, 5465-5479.  
15911625 M.D.Vázquez-Novelle, V.Esteban, A.Bueno, and M.P.Sacristán (2005).
Functional homology among human and fission yeast Cdc14 phosphatases.
  J Biol Chem, 280, 29144-29150.  
14765109 B.A.Wolfe, and K.L.Gould (2004).
Fission yeast Clp1p phosphatase affects G2/M transition and mitotic exit through Cdc25p inactivation.
  EMBO J, 23, 919-929.  
15251038 B.K.Kaiser, M.V.Nachury, B.E.Gardner, and P.K.Jackson (2004).
Xenopus Cdc14 alpha/beta are localized to the nucleolus and centrosome and are required for embryonic cell division.
  BMC Cell Biol, 5, 27.  
15303097 E.T.Kipreos (2004).
Developmental quiescence: Cdc14 moonlighting in G1.
  Nat Cell Biol, 6, 693-695.  
15568976 F.Stegmeier, and A.Amon (2004).
Closing mitosis: the functions of the Cdc14 phosphatase and its regulation.
  Annu Rev Genet, 38, 203-232.  
15362113 G.Nalepa, and J.W.Harper (2004).
Visualization of a highly organized intranuclear network of filaments in living mammalian cells.
  Cell Motil Cytoskeleton, 59, 94.  
15380095 M.K.Balasubramanian, E.Bi, and M.Glotzer (2004).
Comparative analysis of cytokinesis in budding yeast, fission yeast and animal cells.
  Curr Biol, 14, R806-R818.  
15282614 M.Mishima, V.Pavicic, U.Grüneberg, E.A.Nigg, and M.Glotzer (2004).
Cell cycle regulation of central spindle assembly.
  Nature, 430, 908-913.  
15128740 W.Q.Wang, J.Bembenek, K.R.Gee, H.Yu, H.Charbonneau, and Z.Y.Zhang (2004).
Kinetic and mechanistic studies of a cell cycle protein phosphatase Cdc14.
  J Biol Chem, 279, 30459-30468.  
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.