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(-) Description

Title :  STRUCTURAL ANALYSIS OF LEISHMANIA MAJOR UBIQUITIN CONJUGATING ENZYME E2
 
Authors :  Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp)
Date :  31 Dec 04  (Deposition) - 22 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Sgpp, Structural Genomics, Psi, Protein Structure Initiative, Ubiquitin Conjugating Enzyme, Structural Genomics Of Pathogenic Protozoa Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Bosch, W. G. J. Hol
Structural Analysis Of Leishmania Major Ubiquitin Conjugating Enzyme E2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITIN CARRIER PROTEIN 4
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET14B
    Expression System StrainBL21STAR(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificLEISHMANIA MAJOR
    Organism Taxid5664
    Other DetailsT7 SYSTEM

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)ABC
Biological Unit 2 (2x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:123 , HOH A:676 , ARG B:23BINDING SITE FOR RESIDUE CL B 400
2AC2SOFTWAREASN B:123 , HOH B:521 , ARG C:23BINDING SITE FOR RESIDUE CL C 500
3AC3SOFTWAREARG A:23 , ASN C:123 , HOH C:633BINDING SITE FOR RESIDUE CL A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YF9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:67 -Pro A:68
2Tyr B:67 -Pro B:68
3Tyr C:67 -Pro C:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YF9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YF9)

(-) Exons   (0, 0)

(no "Exon" information available for 1YF9)

(-) Sequences/Alignments

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:158
 aligned with Q4Q5L3_LEIMA | Q4Q5L3 from UniProtKB/TrEMBL  Length:234

    Alignment length:158
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158        
         Q4Q5L3_LEIMA     9 SNRRREMDYMRLCNSTRKVYPSDTVAEFWVEFKGPEGTPYEDGTWMLHVQLPSDYPFKSPSIGFCNRILHPNVDERSGSVCLDVINQTWTPMYQLENIFDVFLPQLLRYPNPSDPLNVQAAHLLHADRVGFDALLREHVSTHATPQKALESIPEAYRP 166
               SCOP domains d1yf9a1 A:13-170 Ubiquitin conjugating enzyme, UBC                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....eee.....eeeeeee..........eeeeeee..........eeee................hhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yf9 A  13 SNRRREMDYMRLCNSTRKVYPSDTVAEFWVEFKGPEGTPYEDGTWMLHVQLPSDYPFKSPSIGFCNRILHPNVDERSGSVCLDVINQTWTPMYQLENIFDVFLPQLLRYPNPSDPLNVQAAHLLHADRVGFDALLREHVSTHATPQKALESIPEAYRP 170
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with Q4Q5L3_LEIMA | Q4Q5L3 from UniProtKB/TrEMBL  Length:234

    Alignment length:160
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166
         Q4Q5L3_LEIMA     7 LRSNRRREMDYMRLCNSTRKVYPSDTVAEFWVEFKGPEGTPYEDGTWMLHVQLPSDYPFKSPSIGFCNRILHPNVDERSGSVCLDVINQTWTPMYQLENIFDVFLPQLLRYPNPSDPLNVQAAHLLHADRVGFDALLREHVSTHATPQKALESIPEAYRP 166
               SCOP domains d1yf9b_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh....eee.....eeeeeee..........eeeeeee..........eeee................hhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yf9 B  11 LRSNRRREMDYMRLCNSTRKVYPSDTVAEFWVEFKGPEGTPYEDGTWMLHVQLPSDYPFKSPSIGFCNRILHPNVDERSGSVCLDVINQTWTPMYQLENIFDVFLPQLLRYPNPSDPLNVQAAHLLHADRVGFDALLREHVSTHATPQKALESIPEAYRP 170
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain C from PDB  Type:PROTEIN  Length:159
 aligned with Q4Q5L3_LEIMA | Q4Q5L3 from UniProtKB/TrEMBL  Length:234

    Alignment length:159
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158         
         Q4Q5L3_LEIMA     9 SNRRREMDYMRLCNSTRKVYPSDTVAEFWVEFKGPEGTPYEDGTWMLHVQLPSDYPFKSPSIGFCNRILHPNVDERSGSVCLDVINQTWTPMYQLENIFDVFLPQLLRYPNPSDPLNVQAAHLLHADRVGFDALLREHVSTHATPQKALESIPEAYRPH 167
               SCOP domains d1yf9c_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -UQ_con-1yf9C01 C:14-151                                                                                                                   -------------------- Pfam domains (1)
           Pfam domains (2) -UQ_con-1yf9C02 C:14-151                                                                                                                   -------------------- Pfam domains (2)
           Pfam domains (3) -UQ_con-1yf9C03 C:14-151                                                                                                                   -------------------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhh....eee.....eeeeeee..........eeeeeee..........eeee................hhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yf9 C  13 SNRRREMDYMRLCNSTRKVYPSDTVAEFWVEFKGPEGTPYEDGTWMLHVQLPSDYPFKSPSIGFCNRILHPNVDERSGSVCLDVINQTWTPMYQLENIFDVFLPQLLRYPNPSDPLNVQAAHLLHADRVGFDALLREHVSTHATPQKALESIPEAYRPH 171
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162         

   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)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YF9)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: UBC (69)
(-)
Family: UQ_con (55)
1aUQ_con-1yf9C01C:14-151
1bUQ_con-1yf9C02C:14-151
1cUQ_con-1yf9C03C:14-151

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q4Q5L3_LEIMA | Q4Q5L3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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.
biological process
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    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.

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