3E95 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE PLASMODIUM FALCIPARUM UBIQUITIN CONJUGATING ENZYME COMPLEX, PFUBC13-PFUEV1A

Authors :   A. K. Wernimont, A. Lam, A. Ali, S. Brokx, Y. H. Lin, Y. Zhao, J. Lew, M. Ravichandran, G. Wasney, M. Vedadi, I. Kozieradzki, M. Schapira, A. Bochkarev, M. Wilkstrom, C. Bountra, C. H. Arrowsmith, A. M. Edward W. Qiu, V. B. Brand, Structural Genomics Consortium (Sgc)

Date :   21 Aug 08 (Deposition) - 30 Sep 08 (Release) - 18 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Malaria Ubiquitin Complex Structural Genomics, Ligase, Ubl Conjugation Pathway, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Wernimont, A. Lam, A. Ali, S. Brokx, Y. H. Lin, Y. Zhao, J. Lew, M. Ravichandran, G. Wasney, M. Vedadi, I. Kozieradzki, M. Schapira, A. Bochkarev, M. Wilkstrom, C. Bountra, C. H. Arrowsmith, A. M. Edwards, R. Hui, W. Qiu, V. B. Brand
Crystal Structure Of The Plasmodium Falciparum Ubiquitin Conjugating Enzyme Complex, Pfubc13-Pfuev1A
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:147
 aligned with Q8I3J4_PLAF7 | Q8I3J4 from UniProtKB/TrEMBL  Length:152

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
         Q8I3J4_PLAF7     3 IPRRITKETQNLANEPPPGIMAVPVPENYRHFNILINGPDGTPYEGGTYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKLGRICLDILKDKWSPALQIRTVLLSIQALLSSPEPDDPLDSKVAEHFKQDKNDAEHVARQWNKIYANNN 150
               SCOP domains d3e95a_ A: automated matches                                                                                                                         SCOP domains
               CATH domains 3e95A00 A:2-149 Ubiquitin Conjugating Enzyme                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee....................-.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e95 A   2 IPRRITKETQNLANEPPPGIMAVPVPENYRHFNILINGPDGTPYEGGTYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKLGRICLDIL-DKWSPALQIRTVLLSIQALLSSPEPDDPLDSKVAEHFKQDKNDAEHVARQWNKIYANNN 149
                                    11        21        31        41        51        61        71        81       |91       101       111       121       131       141        
                                                                                                                  89 |                                                          
                                                                                                                    91

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with Q8I3J4_PLAF7 | Q8I3J4 from UniProtKB/TrEMBL  Length:152

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
         Q8I3J4_PLAF7     3 IPRRITKETQNLANEPPPGIMAVPVPENYRHFNILINGPDGTPYEGGTYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKLGRICLDILKDKWSPALQIRTVLLSIQALLSSPEPDDPLDSKVAEHFKQDKNDAEHVARQWNKIYANNN 150
               SCOP domains d3e95b_ B: automated matches                                                                                                                         SCOP domains
               CATH domains 3e95B00 B:2-149 Ubiquitin Conjugating Enzyme                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.....--.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e95 B   2 IPRRITKETQNLANEPPPGIMAVPVPENYRHFNILINGPDGTPYEGGTYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKLGRICLDILKDKWSPALQIRTVLLSIQALLSSPEPDD--DSKVAEHFKQDKNDAEHVARQWNKIYANNN 149
                                    11        21        31        41        51        61        71        81        91       101       111     | 121       131       141        
                                                                                                                                             117  |                             
                                                                                                                                                120

Chain C from PDB  Type:PROTEIN  Length:138
 aligned with O97241_PLAF7 | O97241 from UniProtKB/TrEMBL  Length:142

    Alignment length:138
                                    12        22        32        42        52        62        72        82        92       102       112       122       132        
         O97241_PLAF7     3 EVIVPRSFRLLDELERGQKGNVSEGVSFGLESADDITLSNWSCTIFGQPGTVFENRIYSLTIFCDDNYPDSPPTVKFDTKIEMSCVDNCGRVIKNNLHILKNWNRNYTIETILISLRQEMLSSANKRLPQPNEGEVYS 140
               SCOP domains d3e95c_ C: automated matches                                                                                                               SCOP domains
               CATH domains 3e95C00 C:21-158 Ubiquitin Conjugating Enzyme                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.....eeeee.........eeeeeee..........eeeeeee..........eeee...............hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3e95 C  21 EVIVPRSFRLLDELERGQKGNVSEGVSFGLESADDITLSNWSCTIFGQPGTVFENRIYSLTIFCDDNYPDSPPTVKFDTKIEMSCVDNCGRVIKNNLHILKNWNRNYTIETILISLRQEMLSSANKRLPQPNEGEVYS 158
                                    30        40        50        60        70        80        90       100       110       120       130       140       150

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 '\|'

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (1, 3)

Pfam Domains (0, 0)

Gene Ontology (10, 17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q8I3J4_PLAF7 | Q8I3J4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0006301	postreplication repair	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
	GO:0070534	protein K63-linked ubiquitination	A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Chain C (O97241_PLAF7 | O97241)

molecular function
	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:0006301	postreplication repair	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
	GO:0070534	protein K63-linked ubiquitination	A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
	GO:0006511	ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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