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PDBsum entry 2oyc
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Hydrolase PDB id
2oyc

 

 

 

 

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Contents
Protein chain
292 a.a. *
Ligands
WO4
Metals
_NA
Waters ×168
* Residue conservation analysis
PDB id:
2oyc
Name: Hydrolase
Title: Crystal structure of human pyridoxal phosphate phosphatase
Structure: Pyridoxal phosphate phosphatase. Chain: a. Synonym: plp phosphatase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pdxp, plp, plpp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.72Å     R-factor:   0.193     R-free:   0.223
Authors: U.A.Ramagopal,J.Freeman,M.Izuka,R.Toro,J.M.Sauder,S.K.Burley, S.C.Almo,New York Sgx Research Center For Structural Genomics (Nysgxrc)
Key ref: S.C.Almo et al. (2007). Structural genomics of protein phosphatases. J Struct Funct Genomics, 8, 121-140. PubMed id: 18058037
Date:
21-Feb-07     Release date:   13-Mar-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q96GD0  (PLPP_HUMAN) -  Chronophin from Homo sapiens
Seq:
Struc: 		296 a.a.
292 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:
1. O-phospho-L-seryl-[protein] + H2O = L-seryl-[protein] + phosphate
2. O-phospho-L-threonyl-[protein] + H2O = L-threonyl-[protein] + phosphate
O-phospho-L-seryl-[protein]
 + H2O
 = L-seryl-[protein]
 + phosphate
O-phospho-L-threonyl-[protein]
 + H2O
 = L-threonyl-[protein]
 + phosphate
   Enzyme class 2: E.C.3.1.3.74  - pyridoxal phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: pyridoxal 5'-phosphate + H2O = pyridoxal + phosphate
pyridoxal 5'-phosphate
 + H2O
 = pyridoxal
 + phosphate
      Cofactor: Mg(2+)
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

 

 
    reference    
 
 
J Struct Funct Genomics 8:121-140 (2007)
PubMed id: 18058037  
 
 
Structural genomics of protein phosphatases.
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, S.K.Burley.
 
  ABSTRACT  
 
The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22918415 K.Block, and Y.Gorin (2012).
Aiding and abetting roles of NOX oxidases in cellular transformation.
  Nat Rev Cancer, 12, 627-637.  
21543850 G.T.Lountos, J.E.Tropea, and D.S.Waugh (2011).
Structure of human dual-specificity phosphatase 27 at 2.38 Å resolution.
  Acta Crystallogr D Biol Crystallogr, 67, 471-479.
PDB code: 2y96
21220116 J.King-Scott, P.V.Konarev, S.Panjikar, R.Jordanova, D.I.Svergun, and P.A.Tucker (2011).
Structural characterization of the multidomain regulatory protein Rv1364c from Mycobacterium tuberculosis.
  Structure, 19, 56-69.  
21240543 M.B.Karmacharya, and J.W.Soh (2011).
Bioinformatic identification of novel protein phosphatases in the dog genome.
  Mol Cell Biochem, 351, 149-156.  
20594956 B.Szöör (2010).
Trypanosomatid protein phosphatases.
  Mol Biochem Parasitol, 173, 53-63.  
19489729 A.Edwards (2009).
Large-scale structural biology of the human proteome.
  Annu Rev Biochem, 78, 541-568.  
19167335 A.J.Barr, E.Ugochukwu, W.H.Lee, O.N.King, P.Filippakopoulos, I.Alfano, P.Savitsky, N.A.Burgess-Brown, S.Müller, and S.Knapp (2009).
Large-scale structural analysis of the classical human protein tyrosine phosphatome.
  Cell, 136, 352-363.
PDB codes: 2ahs 2b49 2cfv 2cjz 2gjt 2h4v 2i75 2jjd 2nlk 2nz6 2oc3 2ooq 2p6x 2pa5 2qep 3b7o
19578332 G.Molina, A.Vogt, A.Bakan, W.Dai, P.Queiroz de Oliveira, W.Znosko, T.E.Smithgall, I.Bahar, J.S.Lazo, B.W.Day, and M.Tsang (2009).
Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages.
  Nat Chem Biol, 5, 680-687.  
19770498 G.T.Lountos, J.E.Tropea, S.Cherry, and D.S.Waugh (2009).
Overproduction, purification and structure determination of human dual-specificity phosphatase 14.
  Acta Crystallogr D Biol Crystallogr, 65, 1013-1020.
PDB code: 2wgp
19426233 K.Chattopadhyay, E.Lazar-Molnar, Q.Yan, R.Rubinstein, C.Zhan, V.Vigdorovich, U.A.Ramagopal, J.Bonanno, S.G.Nathenson, and S.C.Almo (2009).
Sequence, structure, function, immunity: structural genomics of costimulation.
  Immunol Rev, 229, 356-386.  
19898420 K.Melcher, L.M.Ng, X.E.Zhou, F.F.Soon, Y.Xu, K.M.Suino-Powell, S.Y.Park, J.J.Weiner, H.Fujii, V.Chinnusamy, A.Kovach, J.Li, Y.Wang, J.Li, F.C.Peterson, D.R.Jensen, E.L.Yong, B.F.Volkman, S.R.Cutler, J.K.Zhu, and H.E.Xu (2009).
A gate-latch-lock mechanism for hormone signalling by abscisic acid receptors.
  Nature, 462, 602-608.  
19818631 M.S.Gentry, J.E.Dixon, and C.A.Worby (2009).
Lafora disease: insights into neurodegeneration from plant metabolism.
  Trends Biochem Sci, 34, 628-639.  
19219566 U.Pieper, R.Chiang, J.J.Seffernick, S.D.Brown, M.E.Glasner, L.Kelly, N.Eswar, J.M.Sauder, J.B.Bonanno, S.Swaminathan, S.K.Burley, X.Zheng, M.R.Chance, S.C.Almo, J.A.Gerlt, F.M.Raushel, M.P.Jacobson, P.C.Babbitt, and A.Sali (2009).
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
  J Struct Funct Genomics, 10, 107-125.  
18298671 D.Moes, A.Himmelbach, A.Korte, G.Haberer, and E.Grill (2008).
Nuclear localization of the mutant protein phosphatase abi1 is required for insensitivity towards ABA responses in Arabidopsis.
  Plant J, 54, 806-819.  
18184575 S.K.Burley, A.Joachimiak, G.T.Montelione, and I.A.Wilson (2008).
Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers.
  Structure, 16, 5.  
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.

 

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