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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KELCH DOMAIN OF HUMAN KBTBD5
 
Authors :  P. Canning, V. Ayinampudi, T. Krojer, C. Strain-Damerell, J. Raynor, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, A. N. Bulloc Structural Genomics Consortium (Sgc)
Date :  30 Apr 12  (Deposition) - 09 May 12  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Binding, Cytoskeleton, Kelch Repeat (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Canning, C. D. O. Cooper, T. Krojer, J. W. Murray, A. C. W. Pike, A. Chaikuad, T. Keates, C. Thangaratnarajah, V. Hojzan, B. D. Marsden O. Gileadi, S. Knapp, F. Von Delft, A. N. Bullock
Structural Basis For Cul3 Assembly With The Btb-Kelch Family Of E3 Ubiquitin Ligases.
J. Biol. Chem. V. 288 7803 2013
PubMed-ID: 23349464  |  Reference-DOI: 10.1074/JBC.M112.437996

(-) Compounds

Molecule 1 - KELCH REPEAT AND BTB DOMAIN-CONTAINING PROTEIN 5
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-CTHF
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    Expression System Vector TypePLASMID
    FragmentKELCH DOMAIN, RESIDUES 314-616
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCYS 340 WAS OXIDISED IN THE CRYSTAL STRUCTURE.
    Other Details - SourceMAMMALIAN GENE COLLECTION (MGC)
    SynonymKBTBD5, SARCOSYNAPSIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
2EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:346 , TYR A:381 , GLU A:546 , HOH A:2048 , HOH A:2226BINDING SITE FOR RESIDUE EDO A1622
2AC2SOFTWAREASN A:412 , ARG A:427 , CYS A:428 , ARG A:437 , VAL A:451 , SER A:472BINDING SITE FOR RESIDUE EDO A1623

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Asymmetric/Biological Unit (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_030214N345SKLH40_HUMANPolymorphism6805421AS345S
02UniProtVAR_069841P397LKLH40_HUMANDisease (NEM8)773649133AP397L
03UniProtVAR_069842H455RKLH40_HUMANDisease (NEM8)770866675AH455R
04UniProtVAR_069843G469CKLH40_HUMANDisease (NEM8)367579275AG469C
05UniProtVAR_077951R500CKLH40_HUMANUnclassified (NEM8)758188096AR500C
06UniProtVAR_077952A505PKLH40_HUMANDisease (NEM8)  ---AA505P
07UniProtVAR_069844T506PKLH40_HUMANDisease (NEM8)778022582AT506P
08UniProtVAR_069845E528KKLH40_HUMANDisease (NEM8)397509419AE528K
09UniProtVAR_069846A538PKLH40_HUMANDisease (NEM8)397509421AA538P
10UniProtVAR_069847E588KKLH40_HUMANDisease (NEM8)201856772AE588K
11UniProtVAR_030215C617RKLH40_HUMANPolymorphism123509AR617R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ASC)

(-) 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:308
 aligned with KLH40_HUMAN | Q2TBA0 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:308
                                   323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613        
          KLH40_HUMAN   314 MFLQDLIFMISEEGAVAYDPAANECYCASLSNQVPKNHVSLVTKENQVFVAGGLFYNEDNKEDPMSAYFLQFDHLDSEWLGMPPLPSPRCLFGLGEALNSIYVVGGREIKDGERCLDSVMCYDRLSFKWGESDPLPYVVYGHTVLSHMDLVYVIGGKGSDRKCLNKMCVYDPKKFEWKELAPMQTARSLFGATVHDGRIIVAAGVTDTGLTSSAEVYSITDNKWAPFEAFPQERSSLSLVSLVGTLYAIGGFATLETESGELVPTELNDIWRYNEEEKKWEGVLREIAYAAGATFLPVRLNVLCLTKM 621
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeee....eeeeee........eeeee.....eeeeeeeee........eeeeeeeee....eeee.......ee..eeeee..eeeee..ee..........eeeee....eeee...........eeeee..eeeee............eeeee....eeee...........eeeee..eeeeeeee....eeeeeeeee....eeeee..........eeeee..eeeeeeeeeeee.....eeeeeeeeeeeee....eeeeee.........eeeeeeehhhhhee. Sec.struct. author
                 SAPs(SNPs) -------------------------------S---------------------------------------------------L---------------------------------------------------------R-------------C------------------------------C----PP---------------------K---------P-------------------------------------------------K----------------------------R---- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4asc A 314 MFLQDLIFMISEEGAVAYDPAANECYcASLSSQVPKNHVSLVTKENQVFVAGGLFYNEDNKEDPMSAYFLQFDHLDSEWLGMPPLPSPRCLFGLGEALNSIYVVGGREIKDGERCLDSVMCYDRLSFKWGESDPLPYVVYGHTVLSHMDLVYVIGGKGSDRKCLNKMCVYDPKKFEWKELAPMQTARSLFGATVHDGRIIVAAGVTDTGLTSSAEVYSITDNKWAPFEAFPQERSSLSLVSLVGTLYAIGGFATLETESGELVPTELNDIWRYNEEEKKWEGVLREIAYAAGATFLPVRLNVLRLTKM 621
                                   323       333      |343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613        
                                                    340-CSO                                                                                                                                                                                                                                                                                     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4ASC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KLH40_HUMAN | Q2TBA0)
molecular function
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0032435    negative regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0031397    negative regulation of protein ubiquitination    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0048741    skeletal muscle fiber development    The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
cellular component
    GO:0031672    A band    The dark-staining region of a sarcomere, in which myosin thick filaments are present; the center is traversed by the paler H zone, which in turn contains the M line.
    GO:0031463    Cul3-RING ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul3 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a BTB-domain-containing protein.
    GO:0031674    I band    A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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