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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VIRAL ZALPHA DOMAIN BOUND TO LEFT-HANDED Z-DNA
 
Authors :  S. C. Ha, D. Van Quyen, C. A. Wu, K. Lowenhaupt, A. Rich, Y. G. Kim, K. K. Kim
Date :  20 Feb 04  (Deposition) - 17 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein/Z-Dna Complex, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Ha, N. K. Lokanath, D. Van Quyen, C. A. Wu, K. Lowenhaupt, A. Rich, Y. G. Kim, K. K. Kim
A Poxvirus Protein Forms A Complex With Left-Handed Z-Dna: Crystal Structure Of A Yatapoxvirus Zalpha Bound To Dna.
Proc. Natl. Acad. Sci. Usa V. 101 14367 2004
PubMed-ID: 15448208  |  Reference-DOI: 10.1073/PNAS.0405586101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*T*CP*GP*CP*GP*CP*G)-3'
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 34L PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL ZALPHA DOMAIN
    Organism Scientific: YABA-LIKE DISEASE VIRUS
    Organism Taxid: 132475

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1SFU)

(-) Sites  (0, 0)

(no "Site" information available for 1SFU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:65 -Pro A:66
2Asn B:65 -Pro B:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SFU)

(-) Exons   (0, 0)

(no "Exon" information available for 1SFU)

(-) 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:70
 aligned with Q9DHS8_YLDV | Q9DHS8 from UniProtKB/TrEMBL  Length:185

    Alignment length:70
                                    15        25        35        45        55        65        75
           Q9DHS8_YLDV    6 CTVNDAEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSNPPKWFKNYNC 75
               SCOP domains d1sfua_ A: 34L                                                         SCOP domains
               CATH domains 1sfuA00 A:6-75 'winged helix' repressor DNA binding domain             CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhh..eeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  1sfu A  6 CTVNDAEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSNPPKWFKNYNC 75
                                    15        25        35        45        55        65        75


Chain B from PDB  Type:PROTEIN  Length:70
 aligned with Q9DHS8_YLDV | Q9DHS8 from UniProtKB/TrEMBL  Length:185

    Alignment length:70
                                    15        25        35        45        55        65        75
           Q9DHS8_YLDV    6 CTVNDAEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSNPPKWFKNYNC 75
               SCOP domains d1sfub_ B: 34L                                                         SCOP domains
               CATH domains 1sfuB00 B:6-75 'winged helix' repressor DNA binding domain             CATH domains
           Pfam domains (1) --------------z-alpha-1sfuB01 B:20-72                              --- Pfam domains (1)
           Pfam domains (2) --------------z-alpha-1sfuB02 B:20-72                              --- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhh.....eehhhhhhhhh..hhhhhhhhhhhhhhh..eeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  1sfu B  6 CTVNDAEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSNPPKWFKNYNC 75
                                    15        25        35        45        55        65        75


Chain C from PDB  Type:DNA  Length:6
                                     
                  1sfu C  1 CGCGCG  6


Chain D from PDB  Type:DNA  Length:6
                                     
                  1sfu D  1 CGCGCG  6
   Legend:   → Mismatch (orange background)
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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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9DHS8_YLDV | Q9DHS8)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003726    double-stranded RNA adenosine deaminase activity    Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a double-stranded RNA molecule.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
biological process
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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.

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  Cis Peptide Bonds
    Asn A:65 - Pro A:66   [ RasMol ]  
    Asn B:65 - Pro B:66   [ RasMol ]  
 

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