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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MMS2/UBC13 - NSC697923
 
Authors :  C. D. Hodge, R. A. Edwards, J. N. M. Glover
Date :  28 Jan 14  (Deposition) - 06 May 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  E2 Ubiquitin Conjugating Enzyme, E1, E3, Ubiquitin, Covalent Adduct, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Hodge, R. A. Edwards, C. J. Markin, D. Mcdonald, M. Pulvino, M. S. Huen, J. Zhao, L. Spyracopoulos, M. J. Hendzel, J. N. Glover
Covalent Inhibition Of Ubc13 Affects Ubiquitin Signaling An Reveals Active Site Elements Important For Targeting.
Acs Chem. Biol. V. 10 1718 2015
PubMed-ID: 25909880  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B00222

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MMS2, UBE2V2, UEV2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DDVIT 1, ENTEROCYTE DIFFERENTIATION-ASSOCIATED FACTOR 1, EDAF-1, ENTEROCYTE DIFFERENTIATION-PROMOTING FACTOR 1, EDPF-1, MMS2 HOMOLOG, VITAMIN D3-INDUCIBLE PROTEIN
 
Molecule 2 - UBIQUITIN-CONJUGATING ENZYME E2 N
    Chains: B
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BLU, UBE2N
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BENDLESS-LIKE UBIQUITIN-CONJUGATING ENZYME, UBC13, UBCH13, UBIQUITIN CARRIER PROTEIN N, UBIQUITIN-PROTEIN LIGASE N

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2N2F1Ligand/Ion2-[(4-METHYLPHENYL)SULFONYL]-5-NITROFURAN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:60 , ILE A:62 , GLY A:90 , ILE A:91 , ASN A:92 , ASN A:93 , HOH A:379 , HOH A:399BINDING SITE FOR RESIDUE GOL A 201
2AC2SOFTWAREPRO B:78 , ASN B:79 , VAL B:80 , ASP B:81 , ARG B:85 , ILE B:86 , CYS B:87 , LEU B:121 , ALA B:122 , ASN B:123 , HOH B:305BINDING SITE FOR RESIDUE N2F B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ONM)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:73 -Pro A:74
2Tyr B:62 -Pro B:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ONM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ONM)

(-) Exons   (0, 0)

(no "Exon" information available for 4ONM)

(-) 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:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.....eeeee.........eeeeeee..........eeeeeee..........eeee................hhhhhhhhhh.....hhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4onm A   6 GVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN 145
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145


Chain B from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4onm B   2 AGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4ONM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ONM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ONM)

(-) Gene Ontology  (50, 67)

Asymmetric/Biological Unit(hide GO term definitions)

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    Tyr A:73 - Pro A:74   [ RasMol ]  
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  4onm
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  UB2V2_HUMAN | Q15819
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  UBE2N_HUMAN | P61088
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  6.3.2.19
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UB2V2_HUMAN | Q15819: 1j74 1j7d 1zgu 3von 4nr3 4nrg 4nri 4onl 4onn 4orh 5ait
        UBE2N_HUMAN | P61088: 1j7d 2c2v 3hct 3hcu 3von 3w31 4dhi 4dhj 4dhz 4ip3 4nr3 4nrg 4nri 4onl 4onn 4orh 4tkp 4whv 5ait 5aiu 5eya

(-) Related Entries Specified in the PDB File

4onl 4onn