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(-) Description

Title :  CRYSTAL STRUCTURE OF BURKHOLDERIA PSEUDOMALLEI EFFECTOR PROTEIN CHBP IN COMPLEX WITH UBIQUITIN
 
Authors :  Q. Yao, J. Cui, Y. Zhu, F. Shao
Date :  30 Sep 12  (Deposition) - 21 Nov 12  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ubiquitin/Nedd8 Deamidase, Ubiquitin, Nedd8, 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
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 78-328
    Gene: BPSS1385
    Mutation: YES
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 272560
    Strain: K96243
    Synonym: CHBP
 
Molecule 2 - POLYUBIQUITIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-76
    Gene: SCD2, UBI4, YLL039C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: UBIQUITIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:238 , LYS A:293 , ASP A:295BINDING SITE FOR RESIDUE PEG A 401
2AC2SOFTWAREARG A:81 , ASN A:199 , ASP A:313 , PHE A:314BINDING SITE FOR RESIDUE FMT A 402
3AC3SOFTWAREALA A:146 , ARG B:42 , ARG B:72 , ARG B:74 , GLY B:75 , HOH B:206 , HOH B:207BINDING SITE FOR RESIDUE PO4 B 101
4AC4SOFTWAREASN A:138 , LEU A:142 , ILE B:44 , PHE B:45 , ALA B:46 , THR B:66 , HIS B:68BINDING SITE FOR RESIDUE FMT B 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HCN)

(-) 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:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...........hhhhhhhhhhhhhhh.....hhhhh......hhhhhhh......eeeeeeee....eeeeeee.....eee............hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hcn 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:77
                                                                                                             
               SCOP domains d4hcnb_ B: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeee.....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4hcn B   0 PMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                     9        19        29        39        49        59        69
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hcn
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 Related Entries

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

UniProtKB/Swiss-Prot
        UBI4P_YEAST | P0CG63: 1otr 1q0w 1wr1 1zgu 1zw7 2g3q 2jt4 2jwz 2kdi 2l00 3cmm 3l0w 3l10 3olm 4nnj 4q5e 4q5h
UniProtKB/TrEMBL
        Q63KH5_BURPS | Q63KH5: 3eir 3eit 3gqm 4hcp

(-) Related Entries Specified in the PDB File

4hcp