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(-) Description

Title :  CRYSTAL STRUCTURE OF BURKHOLDERIA PSEUDOMALLEI EFFECTOR PROTEIN CHBP IN COMPLEX WITH NEDD8
 
Authors :  Q. Yao, F. Shao
Date :  01 Oct 12  (Deposition) - 21 Nov 12  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Deamidase, Alpha/Beta/Alpha Fold, Deamidation, Nedd8/Ubiquitin, Bacterial Cytosol, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Yao, J. Cui, J. Wang, T. Li, X. Wan, T. Luo, Y. N. Gong, Y. Xu, N. Huang, F. Shao
Structural Mechanism Of Ubiquitin And Nedd8 Deamidation Catalyzed By Bacterial Effectors That Induce Macrophage-Specific Apoptosis.
Proc. Natl. Acad. Sci. Usa V. 109 20395 2012
PubMed-ID: 23175788  |  Reference-DOI: 10.1073/PNAS.1210831109

(-) Compounds

Molecule 1 - PUTATIVE ATP/GTP BINDING PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 78-382
    GeneBPSS1385
    MutationYES
    Organism ScientificBURKHOLDERIA PSEUDOMALLEI
    Organism Taxid272560
    StrainK96243
 
Molecule 2 - NEDD8
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 1-76
    GeneNEDD8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEDDYLIN, NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 8, NEDD-8, UBIQUITIN-LIKE PROTEIN NEDD8

 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
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:81 , ASN A:199 , ASP A:313 , PHE A:314 , ARG A:315BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREASN A:107 , ILE A:122 , ALA A:125 , ILE A:126 , THR B:9 , GLY B:10 , LYS B:11BINDING SITE FOR RESIDUE GOL B 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HCP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HCP)

(-) 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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Chain A from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...........hhhhhhhhhhhhhhh.....hhhhh......hhhhhhh......eeeeeeee....eeeeeee.....eee............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hcp A  79 KHRVTLRKATLASLMQSLSGESSNRVMWNDRYDTLLIARDPREIKNAIEKSVTDFGGLENYKELTGGADPFALMTPVAGLSANNIFKLMTEKDVPIDPTSIEYLENTSFAEHVNTLDSHKNYVVIVNDGRLGHKFLIDLPARTAYIIQSDLGGGALPAVRVEDWISRRGSDPVSLDELNQLLSKDFSKMPDDVQTRLLASILQIDKDPHKVDIKKLHLDGKLRFASHEYDFRQFQRNAQYVAGLG 328
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218||     233       243       253       263       273       283       293       303       313       323     
                                                                                                                                                                      219|                                                                                                       
                                                                                                                                                                       225                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4hcpb_ B: Nedd8                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeee....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4hcp B  -1 AAMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL  73
                                     8        18        28        38        48        58        68     

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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEDD8_HUMAN | Q158431ndd 1r4m 1r4n 1xt9 2bkr 2ko3 2n7k 2nvu 3dbh 3dbl 3dbr 3dqv 3gzn 4f8c 4fbj 4p5o
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        Q63KH5_BURPS | Q63KH53eir 3eit 3gqm 4hcn

(-) Related Entries Specified in the PDB File

4hcn