PDBsum entry 2fo3

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Structural genomics, unknown function PDB id
Protein chain
109 a.a. *
Waters ×101
* Residue conservation analysis
PDB id:
Name: Structural genomics, unknown function
Title: Plasmodium vivax ubiquitin conjugating enzyme e2
Structure: Ubiquitin-conjugating enzyme. Chain: a. Engineered: yes
Source: Plasmodium vivax. Organism_taxid: 5855. Gene: ost6, pvx_083175. Expressed in: escherichia coli. Expression_system_taxid: 562. Pet28
Biol. unit: Dimer (from PQS)
1.86Å     R-factor:   0.209     R-free:   0.263
Authors: A.Dong,Y.Zhao,J.Lew,I.Kozieradski,Z.Alam,M.Melone,G.Wasney, M.Vedadi,A.M.Edwards,C.H.Arrowsmith,J.Weigelt,M.Sundstrom, R.Hui,A.Bochkarev,W.Qiu,Structural Genomics Consortium (Sgc
Key ref: M.Vedadi et al. (2007). Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. Mol Biochem Parasitol, 151, 100-110. PubMed id: 17125854
12-Jan-06     Release date:   31-Jan-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
A5K893  (A5K893_PLAVS) -  Ubiquitin-conjugating enzyme E2, putative
215 a.a.
109 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     acid-amino acid ligase activity     1 term  


Mol Biochem Parasitol 151:100-110 (2007)
PubMed id: 17125854  
Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
M.Vedadi, J.Lew, J.Artz, M.Amani, Y.Zhao, A.Dong, G.A.Wasney, M.Gao, T.Hills, S.Brokx, W.Qiu, S.Sharma, A.Diassiti, Z.Alam, M.Melone, A.Mulichak, A.Wernimont, J.Bray, P.Loppnau, O.Plotnikova, K.Newberry, E.Sundararajan, S.Houston, J.Walker, W.Tempel, A.Bochkarev, I.Kozieradzki, A.Edwards, C.Arrowsmith, D.Roos, K.Kain, R.Hui.
Parasites from the protozoan phylum Apicomplexa are responsible for diseases, such as malaria, toxoplasmosis and cryptosporidiosis, all of which have significantly higher rates of mortality and morbidity in economically underdeveloped regions of the world. Advances in vaccine development and drug discovery are urgently needed to control these diseases and can be facilitated by production of purified recombinant proteins from Apicomplexan genomes and determination of their 3D structures. To date, both heterologous expression and crystallization of Apicomplexan proteins have seen only limited success. In an effort to explore the effectiveness of producing and crystallizing proteins on a genome-scale using a standardized methodology, over 400 distinct Plasmodium falciparum target genes were chosen representing different cellular classes, along with select orthologues from four other Plasmodium species as well as Cryptosporidium parvum and Toxoplasma gondii. From a total of 1008 genes from the seven genomes, 304 (30.2%) produced purified soluble proteins and 97 (9.6%) crystallized, culminating in 36 crystal structures. These results demonstrate that, contrary to previous findings, a standardized platform using Escherichia coli can be effective for genome-scale production and crystallography of Apicomplexan proteins. Predictably, orthologous proteins from different Apicomplexan genomes behaved differently in expression, purification and crystallization, although the overall success rates of Plasmodium orthologues do not differ significantly. Their differences were effectively exploited to elevate the overall productivity to levels comparable to the most successful ongoing structural genomics projects: 229 of the 468 target genes produced purified soluble protein from one or more organisms, with 80 and 32 of the purified targets, respectively, leading to crystals and ultimately structures from one or more orthologues.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22993090 A.S.Halavaty, Y.Kim, G.Minasov, L.Shuvalova, I.Dubrovska, J.Winsor, M.Zhou, O.Onopriyenko, T.Skarina, L.Papazisi, K.Kwon, S.N.Peterson, A.Joachimiak, A.Savchenko, and W.F.Anderson (2012).
Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria.
  Acta Crystallogr D Biol Crystallogr, 68, 1359-1370.
PDB codes: 3f09 3hyk 3qmn 4jm7
21287613 A.K.Wernimont, M.Amani, W.Qiu, J.C.Pizarro, J.D.Artz, Y.H.Lin, J.Lew, A.Hutchinson, and R.Hui (2011).
Structures of parasitic CDPK domains point to a common mechanism of activation.
  Proteins, 79, 803-820.
PDB codes: 3k21 3khe
21084289 J.D.Artz, A.K.Wernimont, J.E.Dunford, M.Schapira, A.Dong, Y.Zhao, J.Lew, R.G.Russell, F.H.Ebetino, U.Oppermann, and R.Hui (2011).
Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites.
  J Biol Chem, 286, 3315-3322.
PDB codes: 3ldw 3mav 3ph7
20436473 A.K.Wernimont, J.D.Artz, P.Finerty, Y.H.Lin, M.Amani, A.Allali-Hassani, G.Senisterra, M.Vedadi, W.Tempel, F.Mackenzie, I.Chau, S.Lourido, L.D.Sibley, and R.Hui (2010).
Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium.
  Nat Struct Mol Biol, 17, 596-601.
PDB codes: 3hx4 3hzt 3igo 3ku2
20154706 A.R.Cole, L.P.Lewis, and H.Walden (2010).
The structure of the catalytic subunit FANCL of the Fanconi anemia core complex.
  Nat Struct Mol Biol, 17, 294-298.
PDB code: 3k1l
20189877 J.A.Fernández-Robledo, and G.R.Vasta (2010).
Production of recombinant proteins from protozoan parasites.
  Trends Parasitol, 26, 244-254.  
21078147 M.E.Victor, A.Bengtsson, G.Andersen, D.Bengtsson, J.P.Lusingu, L.S.Vestergaard, D.E.Arnot, T.G.Theander, L.Joergensen, and A.T.Jensen (2010).
Insect cells are superior to Escherichia coli in producing malaria proteins inducing IgG targeting PfEMP1 on infected erythrocytes.
  Malar J, 9, 325.  
20823549 M.Haffke, A.Menzel, Y.Carius, D.Jahn, and D.W.Heinz (2010).
Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides.
  Acta Crystallogr D Biol Crystallogr, 66, 979-987.
PDB codes: 3nh6 3nh9 3nha 3nhb
20637416 M.S.Kimber, A.Y.Yu, M.Borg, E.Leung, H.S.Chan, and W.A.Houry (2010).
Structural and theoretical studies indicate that the cylindrical protease ClpP samples extended and compact conformations.
  Structure, 18, 798-808.
PDB code: 3hln
20466062 M.Vedadi, C.H.Arrowsmith, A.Allali-Hassani, G.Senisterra, and G.A.Wasney (2010).
Biophysical characterization of recombinant proteins: a key to higher structural genomics success.
  J Struct Biol, 172, 107-119.  
20693687 P.K.Fyfe, A.Dawson, M.T.Hutchison, S.Cameron, and W.N.Hunter (2010).
Structure of Staphylococcus aureus adenylosuccinate lyase (PurB) and assessment of its potential as a target for structure-based inhibitor discovery.
  Acta Crystallogr D Biol Crystallogr, 66, 881-888.
PDB code: 2x75
20856875 R.Bakszt, A.Wernimont, A.Allali-Hassani, M.W.Mok, T.Hills, R.Hui, and J.C.Pizarro (2010).
The crystal structure of Toxoplasma gondii pyruvate kinase 1.
  PLoS One, 5, e12736.
PDB codes: 3eoe 3gg8
20652820 S.D.Stojanović, B.L.Zarić, and S.D.Zarić (2010).
Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins.
  J Mol Model, 16, 1743-1751.  
19352432 A.Wernimont, and A.Edwards (2009).
In situ proteolysis to generate crystals for structure determination: an update.
  PLoS ONE, 4, e5094.  
19470714 G.J.Crowther, A.J.Napuli, A.P.Thomas, D.J.Chung, K.V.Kovzun, D.J.Leibly, L.J.Castaneda, J.Bhandari, C.J.Damman, R.Hui, W.G.Hol, F.S.Buckner, C.L.Verlinde, Z.Zhang, E.Fan, and W.C.van Voorhis (2009).
Buffer optimization of thermal melt assays of Plasmodium proteins for detection of small-molecule ligands.
  J Biomol Screen, 14, 700-707.  
19149776 K.Vaughan, M.Blythe, J.Greenbaum, Q.Zhang, B.Peters, D.L.Doolan, and A.Sette (2009).
Meta-analysis of immune epitope data for all Plasmodia: overview and applications for malarial immunobiology and vaccine-related issues.
  Parasite Immunol, 31, 78-97.  
19563628 M.Avril, M.J.Hathaway, M.M.Cartwright, S.O.Gose, D.L.Narum, and J.D.Smith (2009).
Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris.
  Malar J, 8, 143.  
19520088 N.Pulicherla, L.A.Pogorzala, Z.Xu, H.C.O Farrell, F.N.Musayev, J.N.Scarsdale, E.A.Sia, G.M.Culver, and J.P.Rife (2009).
Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.
  J Mol Biol, 391, 884-893.
PDB codes: 3fyc 3fyd
19691130 R.Alag, N.Bharatham, A.Dong, T.Hills, A.Harikishore, A.A.Widjaja, S.G.Shochat, R.Hui, and H.S.Yoon (2009).
Crystallographic structure of the tetratricopeptide repeat domain of Plasmodium falciparum FKBP35 and its molecular interaction with Hsp90 C-terminal pentapeptide.
  Protein Sci, 18, 2115-2124.
PDB code: 2fbn
19197235 W.Qiu, A.Wernimont, K.Tang, S.Taylor, V.Lunin, M.Schapira, S.Fentress, R.Hui, and L.D.Sibley (2009).
Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii.
  EMBO J, 28, 969-979.
PDB codes: 3byv 3dzo
18359859 A.Smeets, E.Loumaye, A.Clippe, J.F.Rees, B.Knoops, and J.P.Declercq (2008).
The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers.
  Protein Sci, 17, 700-710.
PDB codes: 2v2g 2v32 2v41
18541005 B.M.Collins (2008).
The structure and function of the retromer protein complex.
  Traffic, 9, 1811-1822.  
18937256 D.L.Doolan, Y.Mu, B.Unal, S.Sundaresh, S.Hirst, C.Valdez, A.Randall, D.Molina, X.Liang, D.A.Freilich, J.A.Oloo, P.L.Blair, J.C.Aguiar, P.Baldi, D.H.Davies, and P.L.Felgner (2008).
Profiling humoral immune responses to P. falciparum infection with protein microarrays.
  Proteomics, 8, 4680-4694.  
18843360 E.A.Winzeler (2008).
Malaria research in the post-genomic era.
  Nature, 455, 751-756.  
18602399 E.T.Larson, W.Deng, B.E.Krumm, A.Napuli, N.Mueller, W.C.Van Voorhis, F.S.Buckner, E.Fan, A.Lauricella, G.DeTitta, J.Luft, F.Zucker, W.G.Hol, C.L.Verlinde, and E.A.Merritt (2008).
Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity.
  J Mol Biol, 381, 975-988.
PDB codes: 2pgf 2pgr 2qvn
18959795 H.C.O'Farrell, Z.Xu, G.M.Culver, and J.P.Rife (2008).
Sequence and structural evolution of the KsgA/Dim1 methyltransferase family.
  BMC Res Notes, 1, 108.  
19101474 J.D.Artz, J.E.Dunford, M.J.Arrowood, A.Dong, M.Chruszcz, K.L.Kavanagh, W.Minor, R.G.Russell, F.H.Ebetino, U.Oppermann, and R.Hui (2008).
Targeting a uniquely nonspecific prenyl synthase with bisphosphonates to combat cryptosporidiosis.
  Chem Biol, 15, 1296-1306.
PDB codes: 2o1o 2q58
18392759 J.Hinojosa-Moya, B.Xoconostle-Cázares, E.Piedra-Ibarra, A.Méndez-Tenorio, W.J.Lucas, and R.Ruiz-Medrano (2008).
Phylogenetic and structural analysis of translationally controlled tumor proteins.
  J Mol Evol, 66, 472-483.  
18282486 J.Weigelt, L.D.McBroom-Cerajewski, M.Schapira, Y.Zhao, C.H.Arrowsmith, and C.H.Arrowmsmith (2008).
Structural genomics and drug discovery: all in the family.
  Curr Opin Chem Biol, 12, 32-39.  
18828893 L.M.Birkholtz, G.Blatch, T.L.Coetzer, H.C.Hoppe, E.Human, E.J.Morris, Z.Ngcete, L.Oldfield, R.Roth, A.Shonhai, L.Stephens, and A.I.Louw (2008).
Heterologous expression of plasmodial proteins for structural studies and functional annotation.
  Malar J, 7, 197.  
18550358 M.S.Jurica (2008).
Detailed close-ups and the big picture of spliceosomes.
  Curr Opin Struct Biol, 18, 315-320.  
18473837 R.Docampo, and S.N.Moreno (2008).
The acidocalcisome as a target for chemotherapeutic agents in protozoan parasites.
  Curr Pharm Des, 14, 882-888.  
18269336 S.N.Moreno, and Z.H.Li (2008).
Anti-infectives targeting the isoprenoid pathway of Toxoplasma gondii.
  Expert Opin Ther Targets, 12, 253-263.  
18268027 T.Tsuboi, S.Takeo, H.Iriko, L.Jin, M.Tsuchimochi, S.Matsuda, E.T.Han, H.Otsuki, O.Kaneko, J.Sattabongkot, R.Udomsangpetch, T.Sawasaki, M.Torii, and Y.Endo (2008).
Wheat germ cell-free system-based production of malaria proteins for discovery of novel vaccine candidates.
  Infect Immun, 76, 1702-1708.  
18186464 W.Tempel, Y.Tong, S.Dimov, A.Bochkarev, and H.Park (2008).
First crystallographic models of human TBC domains in the context of a family-wide structural analysis.
  Proteins, 71, 497-502.  
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
  17329816 G.Guncar, C.I.Wang, J.K.Forwood, T.Teh, A.M.Catanzariti, J.G.Ellis, P.N.Dodds, and B.Kobe (2007).
The use of Co2+ for crystallization and structure determination, using a conventional monochromatic X-ray source, of flax rust avirulence protein.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 209-213.
PDB code: 2opc
17875391 P.Gayathri, H.Balaram, and M.R.Murthy (2007).
Structural biology of plasmodial proteins.
  Curr Opin Struct Biol, 17, 744-754.  
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.