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(-) Description

Title :  SOLUTION STRUCTURE OF THE KSHV K3 N-TERMINAL DOMAIN
 
Authors :  R. B. Dodd, M. D. Allen, S. E. Brown, C. M. Sanderson, L. M. Duncan, P. J. Lehner, M. Bycroft, R. J. Read
Date :  07 May 04  (Deposition) - 01 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (28x)
Keywords :  Zinc-Binding Protein, Ring Domain, Cross-Brace Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. B. Dodd, M. D. Allen, S. E. Brown, C. M. Sanderson, L. M. Duncan, P. J. Lehner, M. Bycroft, R. J. Read
Solution Structure Of The Kaposi'S Sarcoma- Associated Herpesvirus K3 N-Terminal Domain Reveals A Novel E2-Binding C4Hc3-Type Ring Domain
J. Biol. Chem. V. 279 53840 2004
PubMed-ID: 15465811  |  Reference-DOI: 10.1074/JBC.M409662200

(-) Compounds

Molecule 1 - ORF K3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41
    Expression System Taxid: 562
    Expression System Vector: MODIFIED PRSETA
    Fragment: RING FINGER, RESIDUES 1-60
    Organism Common: KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS
    Organism Scientific: HUMAN HERPESVIRUS 8
    Organism Taxid: 37296
    Synonym: K3RING

 Structural Features

(-) Chains, Units

  
NMR Structure (28x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:9 , CYS A:12 , HIS A:34 , CYS A:37BINDING SITE FOR RESIDUE ZN A1061
2AC2SOFTWARECYS A:24 , CYS A:26 , CYS A:50 , CYS A:53BINDING SITE FOR RESIDUE ZN A1062

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VYX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VYX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VYX)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_CHPS51292 Zinc finger RING-CH-type profile.MIR1_HHV8P1-60  1A:1-60

(-) Exons   (0, 0)

(no "Exon" information available for 1VYX)

(-) Sequences/Alignments

NMR Structure
   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:60
 aligned with MIR1_HHV8P | P90495 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:60
                                    10        20        30        40        50        60
            MIR1_HHV8P    1 MEDEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR 60
               SCOP domains d1vyxa_ A: IE1B protein (ORF K3), N-terminal domain          SCOP domains
               CATH domains 1vyxA00 A:1-60 Zinc/RING finger domain, C3HC4 (zinc finger)  CATH domains
               Pfam domains --------RINGv-1vyxA01 A:9-53                         ------- Pfam domains
         Sec.struct. author .......ee....ee............hhhhh.hhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ZF_RING_CH  PDB: A:1-60 UniProt: 1-60                        PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  1vyx A  1 MEDEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR 60
                                    10        20        30        40        50        60
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RING (39)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (MIR1_HHV8P | P90495)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039648    modulation by virus of host protein ubiquitination    Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0039504    suppression by virus of host adaptive immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the adaptive immune response of the host organism, an immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039511    suppression by virus of host interferon receptor activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the functional activity of a host interferon receptor.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0044165    host cell endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1chc EQUINE HERPES VIRUS-1 (C3HC4, OR RING DOMAIN) (NMR, 1 STRUCTURE)