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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN LUBX/LEGU2/LPP2887 U-BOX 1 AND HOMO SAPIENS UBE2D2
 
Authors :  P. J. Stogios, A. T. Quaile, T. Skarina, B. Nocek, R. Di Leo, V. Yim, A. Sa A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  18 Nov 14  (Deposition) - 07 Jan 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Protein, Effector, Activating Enzyme, Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. T. Quaile, M. L. Urbanus, P. J. Stogios, B. Nocek, T. Skarina, A. W. Ensminger, A. Savchenko
Molecular Characterization Of Lubx: Functional Divergence O The U-Box Fold By Legionella Pneumophila.
Structure V. 23 1459 2015
PubMed-ID: 26146184  |  Reference-DOI: 10.1016/J.STR.2015.05.020

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 D2
    ChainsA
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP15TV-LIC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneUBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN 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 LUBX
    ChainsB
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP15TV-LIC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneLUBX, LPP2887
    Organism ScientificLEGIONELLA PNEUMOPHILA
    Organism Taxid297246
    StrainPARIS
    SynonymLEGIONELLA U-BOX PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4WZ3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WZ3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:0 -Met A:1
2Asp A:28 -Asp A:29
3Tyr A:60 -Pro A:61
4Glu B:168 -Thr B:169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WZ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WZ3)

(-) Exons   (0, 0)

(no "Exon" information available for 4WZ3)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.......ee.........eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wz3 A   0 GMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139        

Chain B from PDB  Type:PROTEIN  Length:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh.....hhhhh..........eee.....eeehhhhhhhhh............hhhhhee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh..........eee.....eeehhhhhhhhhhh..ee...ee......ee.hhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wz3 B   4 RNPFDIDHKSKYLREAALEANLSHPETTPTmLTCPIDSGFLKDPVITPEGFVYNKSSILKWLETKKEDPQSRKPLTAKDLQPFPELLIIVNRFVETQTNYEKLKNRLVQNARVAARQKEYTEIPDIFLCPISKTLIKTPVITAQGKVYDQEALSNFLIATGNKDETGKKLSIDDVVVFDELYQ 186
                                    13        23        33|       43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   
                                                         34-MSE                                                                                                                                                    

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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 4WZ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WZ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WZ3)

(-) Gene Ontology  (26, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:28 - Asp A:29   [ RasMol ]  
    Glu B:168 - Thr B:169   [ RasMol ]  
    Gly A:0 - Met A:1   [ RasMol ]  
    Tyr A:60 - Pro A:61   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        LUBX_LEGPA | Q5X1594wz0 4wz2 4xi1
        UB2D2_HUMAN | P628371ur6 1w4u 2clw 2esk 2eso 2esp 2esq 3a33 3jvz 3jw0 3l1y 3tgd 3zni 4a49 4a4b 4a4c 4auq 4ddg 4ddi 4ldt 4v3k 4v3l 5d0k 5d0m 5d1k 5d1l 5d1m 5edv 5mnj 5ulf 5ulh 5ulk

(-) Related Entries Specified in the PDB File

4wz0 U-BOX 1 RELATED ID: MCSG-APC108251 RELATED DB: TARGETTRACK
4wz1 U-BOX 2 (WILD-TYPE)
4wz2 U-BOX 2, ILE175MET MUTANT