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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN MMS2/UBC13 D118G MUTANT
 
Authors :  C. D. Hodge, R. A. Edwards, J. N. M. Glover
Date :  26 Nov 13  (Deposition) - 10 Dec 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ubc13, Mms2, E2, Ubiquitin Conjugating Enzyme, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Rout, C. D. Hodge, C. J. Markin, X. Xu, J. N. Glover, W. Xiao, L. Spyracopoulos
Stochastic Gate Dynamics Regulate The Catalytic Activity Of Ubiquitination Enzymes.
J. Am. Chem. Soc. V. 136 17446 2014
PubMed-ID: 25423605  |  Reference-DOI: 10.1021/JA505440B

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS-P1
    Expression System Strain: BL21(DE3)-RIPL
    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: PHIS-P1
    Expression System Strain: BL21(DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BLU, UBE2N
    Mutation: YES
    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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4NRG)

(-) Sites  (0, 0)

(no "Site" information available for 4NRG)

(-) SS Bonds  (0, 0)

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

(-) 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 4NRG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NRG)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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.....hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nrg 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:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nrg B   2 AGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPGDPNDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    11        21        31        41        51        61        71        81        91       101       111       123       133       143       
                                                                                                                                                120|                           
                                                                                                                                                 123
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  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 4NRG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (50, 67)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 4nrg)
 
  Cis Peptide Bonds
    Tyr A:73 - Pro A:74   [ RasMol ]  
    Tyr B:62 - Pro B:63   [ RasMol ]  
 

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  4nrg
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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 4nri 4onl 4onm 4onn 4orh 5ait
        UBE2N_HUMAN | P61088: 1j7d 2c2v 3hct 3hcu 3von 3w31 4dhi 4dhj 4dhz 4ip3 4nr3 4nri 4onl 4onm 4onn 4orh 4tkp 4whv 5ait 5aiu 5eya

(-) Related Entries Specified in the PDB File

4nr3 4nri