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(-) Description

Title :  STRUCTURE OF THE DNA BINDING DOMAIN OF THE GPNU1 SUBUNIT OF LAMBDA TERMINASE
 
Authors :  T. De Beer, J. Meyer, M. Ortega, Q. Yang, L. Maes, C. Duffy, N. Berton, J. Sippy, M. Overduin, M. Feiss, C. Catalano
Date :  25 May 01  (Deposition) - 14 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Dna Binding Domain, Homodimer, Viral Assembly, Lambda, Winged Helix-Turn-Helix, Terminase, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. De Beer, J. Fang, M. Ortega, Q. Yang, L. Maes, C. Duffy, N. Berton, J. Sippy, M. Overduin, M. Feiss, C. E. Catalano
Insights Into Specific Dna Recognition During The Assembly Of A Viral Genome Packaging Machine.
Mol. Cell V. 9 981 2002
PubMed-ID: 12049735  |  Reference-DOI: 10.1016/S1097-2765(02)00537-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TERMINASE SMALL SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN, RESIDUES 1-68
    Gene: NU1
    Organism Scientific: ENTEROBACTERIA PHAGE LAMBDA
    Organism Taxid: 10710
    Synonym: DNA PACKAGING PROTEIN NU1;
GPNU1 DBD

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1J9I)

(-) Sites  (0, 0)

(no "Site" information available for 1J9I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J9I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J9I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J9I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J9I)

(-) Exons   (0, 0)

(no "Exon" information available for 1J9I)

(-) 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:68
 aligned with TERS_LAMBD | P03707 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:68
                                    10        20        30        40        50        60        
            TERS_LAMBD    1 MEVNKKQLADIFGASIRTIQNWQEQGMPVLRGGGKGNEVLYDSAAVIKWYAERDAEIENEKLRREVEE 68
               SCOP domains d1j9ia_ A: Terminase gpNU1 subunit domain                            SCOP domains
               CATH domains 1j9iA00 A:1-68 'winged helix' repressor DNA binding domain           CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhh..hhhhhhhhh................eeehhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  1j9i A  1 MEVNKKQLADIFGASIRTIQNWQEQGMPVLRGGGKGNEVLYDSAAVIKWYAERDAEIENEKLRREVEE 68
                                    10        20        30        40        50        60        


Chain B from PDB  Type:PROTEIN  Length:68
 aligned with TERS_LAMBD | P03707 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:68
                                    10        20        30        40        50        60        
            TERS_LAMBD    1 MEVNKKQLADIFGASIRTIQNWQEQGMPVLRGGGKGNEVLYDSAAVIKWYAERDAEIENEKLRREVEE 68
               SCOP domains d1j9ib_ B: Terminase gpNU1 subunit domain                            SCOP domains
               CATH domains 1j9iB00 B:1-68 'winged helix' repressor DNA binding domain           CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhh..hhhhhhhhh........hhhhh....ee.hhhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  1j9i B  1 MEVNKKQLADIFGASIRTIQNWQEQGMPVLRGGGKGNEVLYDSAAVIKWYAERDAEIENEKLRREVEE 68
                                    10        20        30        40        50        60
   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  (1, 2)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J9I)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A,B   (TERS_LAMBD | P03707)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0019073    viral DNA genome packaging    The packing of viral DNA into a capsid.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.

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4752 CHEMICAL SHIFT ASSIGNMENT