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Title :   CRYSTAL STRUCTURE OF UBIQUITIN CONJUGATING ENZYME E2 FROM PLASMODIUM FALCIPARUM

Authors :   W. Qiu, A. Dong, Y. Zhao, J. Lew, I. Kozieradski, E. Sundararajan, M. Melone, G. Wasney, M. Vedadi, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, A. Bochkarev, R. Hui, Structural Genomics Consortium (Sgc)

Date :   19 May 06 (Deposition) - 20 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Structural Genomics, Unknown Function, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   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
Genome-Scale Protein Expression And Structural Biology Of Plasmodium Falciparum And Related Apicomplexan Organisms.
Mol. Biochem. Parasitol. V. 151 100 2007
PubMed-ID: 17125854 | Reference-DOI: 10.1016/J.MOLBIOPARA.2006.10.011
(for further references see the PDB file header)

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15-TEV-LIC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUE 115-250
	Gene	:	MAL13P1.227
	Organism Scientific	:	PLASMODIUM FALCIPARUM 3D7
	Organism Taxid	:	36329
	Strain	:	ISOLATE 3D7

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2H2Y)

(no "Site" information available for 2H2Y)

Asymmetric Unit

No.	Residues
1	B:105	-	D:105

Asymmetric Unit

No.	Residues
1	Tyr A:79	-	Pro A:80
2	Tyr B:79	-	Pro B:80
3	Tyr C:79	-	Pro C:80
4	Tyr D:79	-	Pro D:80

(no "SAP(SNP)/Variant" information available for 2H2Y)

(no "PROSITE Motif" information available for 2H2Y)

(no "Exon" information available for 2H2Y)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:133
 aligned with Q8IDP1_PLAF7 | Q8IDP1 from UniProtKB/TrEMBL  Length:278

    Alignment length:133
                                   126       136       146       156       166       176       186       196       206       216       226       236       246   
         Q8IDP1_PLAF7   117 KPSRTVEKHIKTKYNLGNANYRIQKELNNFLKNPPINCTIDVHPSNIRIWIVQYVGLENTIYANEVYKIKIIFPDNYPLKPPIVYFLQKPPKHTHVYSNGDICLSVLGDDYNPSLSISGLILSIISMLSSAKE 249
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee.................hhhhh.......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h2y A   3 KPSRTVEKHIKTKYNLGNANYRIQKELNNFLKNPPINCTIDVHPSNIRIWIVQYVGLENTIYANEVYKIKIIFPDNYPLKPPIVYFLQKPPKHTHVYSNGDICLSVLGDDYNPSLSISGLILSIISMLSSAKE 135
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with Q8IDP1_PLAF7 | Q8IDP1 from UniProtKB/TrEMBL  Length:278

    Alignment length:113
                                   145       155       165       175       185       195       205       215       225       235       245   
         Q8IDP1_PLAF7   136 NYRIQKELNNFLKNPPINCTIDVHPSNIRIWIVQYVGLENTIYANEVYKIKIIFPDNYPLKPPIVYFLQKPPKHTHVYSNGDICLSVLGDDYNPSLSISGLILSIISMLSSAK 248
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....eeeee......eeeeee............eeeeee..........eeee.................hhhhh.......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2h2y B  22 NYRIQKELNNFLKNPPINCTIDVHPSNIRIWIVQYVGLENTIYANEVYKIKIIFPDNYPLKPPIVYFLQKPPKHTHVYSNGDICLSVLGDDYNPSLSISGLILSIISMLSSAK 134
                                    31        41        51        61        71        81        91       101       111       121       131

Chain C from PDB  Type:PROTEIN  Length:113
 aligned with Q8IDP1_PLAF7 | Q8IDP1 from UniProtKB/TrEMBL  Length:278

    Alignment length:113
                                   145       155       165       175       185       195       205       215       225       235       245   
         Q8IDP1_PLAF7   136 NYRIQKELNNFLKNPPINCTIDVHPSNIRIWIVQYVGLENTIYANEVYKIKIIFPDNYPLKPPIVYFLQKPPKHTHVYSNGDICLSVLGDDYNPSLSISGLILSIISMLSSAK 248
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee.................hhhhh.......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2h2y C  22 NYRIQKELNNFLKNPPINCTIDVHPSNIRIWIVQYVGLENTIYANEVYKIKIIFPDNYPLKPPIVYFLQKPPKHTHVYSNGDICLSVLGDDYNPSLSISGLILSIISMLSSAK 134
                                    31        41        51        61        71        81        91       101       111       121       131

Chain D from PDB  Type:PROTEIN  Length:112
 aligned with Q8IDP1_PLAF7 | Q8IDP1 from UniProtKB/TrEMBL  Length:278

    Alignment length:112
                                   145       155       165       175       185       195       205       215       225       235       245  
         Q8IDP1_PLAF7   136 NYRIQKELNNFLKNPPINCTIDVHPSNIRIWIVQYVGLENTIYANEVYKIKIIFPDNYPLKPPIVYFLQKPPKHTHVYSNGDICLSVLGDDYNPSLSISGLILSIISMLSSA 247
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....eeee.......eeeeeee..........eeeeeee..........eeee.................hhhhh.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2h2y D  22 NYRIQKELNNFLKNPPINCTIDVHPSNIRIWIVQYVGLENTIYANEVYKIKIIFPDNYPLKPPIVYFLQKPPKHTHVYSNGDICLSVLGDDYNPSLSISGLILSIISMLSSA 133
                                    31        41        51        61        71        81        91       101       111       121       131

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2H2Y)

(no "CATH Domain" information available for 2H2Y)

(no "Pfam Domain" information available for 2H2Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q8IDP1_PLAF7 | Q8IDP1)

molecular function
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0061630	ubiquitin protein ligase activity	Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
	GO:0000209	protein polyubiquitination	Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0010564	regulation of cell cycle process	Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
	GO:0020011	apicoplast	The plastid organelle found in apicomplexans.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2h2y)

	Sites
(no "Sites" information available for 2h2y)

	Cis Peptide Bonds
		Tyr A:79 - Pro A:80	[ RasMol ]
		Tyr B:79 - Pro B:80	[ RasMol ]
		Tyr C:79 - Pro C:80	[ RasMol ]
		Tyr D:79 - Pro D:80	[ RasMol ]

Biological Units
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	2h2y
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2fo3	PLASMODIUM VIVAX UBIQUITIN CONJUGATING ENZYME E2

Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

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Exons (0, 0)

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