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(-) Description

Title :  CRYSTAL STRUCTURE OF UBCH5B IN COMPLEX WITH THE RING-U5BR FRAGMENT OF AO7 (P199A)
 
Authors :  Y. -H. Liang, S. Li, A. M. Weissman, X. Ji
Date :  08 Oct 13  (Deposition) - 28 Oct 15  (Release) - 30 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ubiquitin Conjugating Enzyme (E2), Ubiquitin Ligase (E3), Ring Finger, Ubiquitination, Ubiquitin, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Li, Y. H. Liang, J. Mariano, M. B. Metzger, D. K. Stringer, V. A. Hristova, J. Li, P. A. Randazzo, Y. C. Tsai, X. Ji, A. M. Weissman
Insights Into Ubiquitination From The Unique Clamp-Like Binding Of The Ring E3 Ao7 To The E2 Ubch5B.
J. Biol. Chem. V. 290 30225 2015
PubMed-ID: 26475854  |  Reference-DOI: 10.1074/JBC.M115.685867

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 D2
    Chains: A
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UBIQUITIN CARRIER PROTEIN D2,UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2,UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2,UBIQUITIN-PROTEIN LIGASE D2,P53-REGULATED UBIQUITIN-CONJUGATING ENZYME 1
 
Molecule 2 - E3 UBIQUITIN-PROTEIN LIGASE RNF25
    Chains: B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 126-258
    Gene: RNF25
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RING FINGER PROTEIN 25

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2OXL1Ligand/IonOXALATE ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:140 , TRP A:141 , LYS A:144 , TYR A:145 , PEG A:202binding site for residue OXL A 201
2AC2SOFTWAREARG A:72 , SER A:80 , TRP A:141 , TYR A:145 , OXL A:201 , HOH A:397binding site for residue PEG A 202
3AC3SOFTWARECYS B:135 , CYS B:138 , HIS B:158 , CYS B:161binding site for residue ZN B 301
4AC4SOFTWARECYS B:153 , HIS B:155 , CYS B:198 , CYS B:201binding site for residue ZN B 302
5AC5SOFTWARETHR B:149 , LYS B:150 , THR B:151 , PRO B:152 , VAL B:206 , GLU B:247 , ARG B:248binding site for residue EDO B 303
6AC6SOFTWAREASN A:41 , GLN A:46 , MET A:147 , LYS B:150 , TYR B:154 , ARG B:248binding site for residue EDO B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D1M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:60 -Pro A:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D1M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D1M)

(-) Exons   (0, 0)

(no "Exon" information available for 5D1M)

(-) 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:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d1m A   2 ALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      


Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eee.....eeehhhhhhhhhhhhhhhhhhh.............hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5d1m B 129 NIPHGQCVICLYGFQEKEAFTKTPCYHYFHCHCLARYIQHMEQELKAQGGVQCAVCREPLVYDLASLKAAPEPQQPMELYQPSAESLRQQEERKRLYQRQQERGGIIDLE 255
                                   138       148       158       168       195       205       215       225       235       245       255
                                                                          177|                                                            
                                                                           195
   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 5D1M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D1M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D1M)

(-) Gene Ontology  (29, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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    Tyr A:60 - Pro A:61   [ RasMol ]  
 

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  UB2D2_HUMAN | P62837
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  6.3.2.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNF25_HUMAN | Q96BH1: 2day 2dmf 5d1k 5d1l
        UB2D2_HUMAN | P62837: 1ur6 1w4u 2clw 2esk 2eso 2esp 2esq 3a33 3jvz 3jw0 3l1y 3tgd 3zni 4a49 4a4b 4a4c 4auq 4ddg 4ddi 4ldt 4v3k 4v3l 4wz3 5d0k 5d0m 5d1k 5d1l 5edv 5mnj 5ulf 5ulh 5ulk

(-) Related Entries Specified in the PDB File

5d1k 5d1l