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(-) Description

Title :  STRUCTURE OF FBXL5 HEMERYTHRIN DOMAIN, C2 CELL
 
Authors :  D. R. Tomchick, R. K. Bruick, J. W. Thompson, C. A. Brautigam
Date :  17 Dec 11  (Deposition) - 25 Jan 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hemerythrin, Alpha Helical Bundle, E3 Ubiquitin Ligase Complex, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Thompson, A. A. Salahudeen, S. Chollangi, J. C. Ruiz, C. A. Brautigam, T. M. Makris, J. D. Lipscomb, D. R. Tomchick, R. K. Bruick
Structural And Molecular Characterization Of Iron-Sensing Hemerythrin-Like Domain Within F-Box And Leucine-Rich Repea Protein 5 (Fbxl5).
J. Biol. Chem. V. 287 7357 2012
PubMed-ID: 22253436  |  Reference-DOI: 10.1074/JBC.M111.308684
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - F-BOX/LRR-REPEAT PROTEIN 5
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGST-PARALLEL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HEMERYTHRIN DOMAIN (UNP RESIDUES 1-161)
    Gene: FBL4, FBL5, FBXL5, FLR1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 5, F-BOX PROTEIN FBL4/FBL5, P45SKP2-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FEO2Ligand/IonMU-OXO-DIIRON
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FEO1Ligand/IonMU-OXO-DIIRON
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FEO1Ligand/IonMU-OXO-DIIRON

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:15 , HIS A:57 , GLU A:58 , GLU A:61 , HIS A:80 , HIS A:126 , GLU A:130BINDING SITE FOR RESIDUE FEO A 201
2AC2SOFTWAREHIS B:15 , HIS B:57 , GLU B:58 , GLU B:61 , HIS B:80 , HIS B:126 , GLU B:130BINDING SITE FOR RESIDUE FEO B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V5X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V5X)

(-) Exons   (0, 0)

(no "Exon" information available for 3V5X)

(-) Sequences/Alignments

Asymmetric 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:151
 aligned with FBXL5_HUMAN | Q9UKA1 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:156
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153      
          FBXL5_HUMAN     4 FPEEVDVFTAPHWRMKQLVGLYCDKLSKTNFSNNNDFRALLQSLYATFKEFKMHEQIENEYIIGLLQQRSQTIYNVHSDNKLSEMLSLFEKGLKNVKNEYEQLNYAKQLKERLEAFTRDFLPHMKEEEEVFQPMLMEYFTYEELKDIKKKVIAQHC 159
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--....---.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v5x A   4 FPEEVDVFTAPHWRMKQLVGLYCDKLSKTNFSNNNDFRALLQSLYATFKEFKMHEQIENEYIIGLLQQRSQ--YNVH---KLSEMLSLFEKGLKNVKNEYEQLNYAKQLKERLEAFTRDFLPHMKEEEEVFQPMLMEYFTYEELKDIKKKVIAQHC 159
                                    13        23        33        43        53        63        73|  |  |  -|       93       103       113       123       133       143       153      
                                                                                                 74 77 80  84                                                                           


Chain B from PDB  Type:PROTEIN  Length:152
 aligned with FBXL5_HUMAN | Q9UKA1 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:157
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       
          FBXL5_HUMAN     4 FPEEVDVFTAPHWRMKQLVGLYCDKLSKTNFSNNNDFRALLQSLYATFKEFKMHEQIENEYIIGLLQQRSQTIYNVHSDNKLSEMLSLFEKGLKNVKNEYEQLNYAKQLKERLEAFTRDFLPHMKEEEEVFQPMLMEYFTYEELKDIKKKVIAQHCS 160
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--....---.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v5x B   4 FPEEVDVFTAPHWRMKQLVGLYCDKLSKTNFSNNNDFRALLQSLYATFKEFKMHEQIENEYIIGLLQQRSQ--YNVH---KLSEMLSLFEKGLKNVKNEYEQLNYAKQLKERLEAFTRDFLPHMKEEEEVFQPMLMEYFTYEELKDIKKKVIAQHCS 160
                                    13        23        33        43        53        63        73|  |  |  -|       93       103       113       123       133       143       153       
                                                                                                 74 77 80  84
   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 3V5X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V5X)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FBXL5_HUMAN | Q9UKA1)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0031146    SCF-dependent proteasomal ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by an SCF (Skp1/Cul1/F-box protein) complex, and mediated by the proteasome.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:1903364    positive regulation of cellular protein catabolic process    Any process that activates or increases the frequency, rate or extent of cellular protein catabolic process.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0019005    SCF ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1).
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FBXL5_HUMAN | Q9UKA1: 3u9j 3u9m 3v5y 3v5z

(-) Related Entries Specified in the PDB File

3v5y 3v5z