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(-) Description

Title :  N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB
 
Authors :  D. Fass, C. E. Bogden, J. M. Berger
Date :  28 Jan 99  (Deposition) - 30 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Helicase, Hexamer, Dna Replication, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Fass, C. E. Bogden, J. M. Berger
Crystal Structure Of The N-Terminal Domain Of The Dnab Hexameric Helicase.
Structure Fold. Des. V. 7 691 1999
PubMed-ID: 10404598  |  Reference-DOI: 10.1016/S0969-2126(99)80090-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNAB HELICASE
    Chains: A, B, C, D
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: HEXAMERS NOT ASSOCIATED IN CRYSTAL

 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 1B79)

(-) Sites  (0, 0)

(no "Site" information available for 1B79)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B79)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B79)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B79)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B79)

(-) Exons   (0, 0)

(no "Exon" information available for 1B79)

(-) 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:102
 aligned with DNAB_ECOLI | P0ACB0 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:102
                                    36        46        56        66        76        86        96       106       116       126  
           DNAB_ECOLI    27 PPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRE 128
               SCOP domains d1b79a_ A: N-terminal domain of DnaB helicase                                                          SCOP domains
               CATH domains 1b79A00 A:26-127 DNAb Helicase; Chain A                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhh....hhh...hhhhhhhhhhhhhhhh.....hhhhhhhhh....hhhh.hhhhhhhhhhh......hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1b79 A  26 PPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRE 127
                                    35        45        55        65        75        85        95       105       115       125  


Chain B from PDB  Type:PROTEIN  Length:103
 aligned with DNAB_ECOLI | P0ACB0 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:103
                                    36        46        56        66        76        86        96       106       116       126   
           DNAB_ECOLI    27 PPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRER 129
               SCOP domains d1b79b_ B: N-terminal domain of DnaB helicase                                                           SCOP domains
               CATH domains 1b79B00 B:26-128 DNAb Helicase; Chain A                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhh....hhh...hhhhhhhhhhhhhhhh.....hhhhhhhhh....hhhh.hhhhhhhhhhh......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1b79 B  26 PPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRER 128
                                    35        45        55        65        75        85        95       105       115       125   


Chain C from PDB  Type:PROTEIN  Length:102
 aligned with DNAB_ECOLI | P0ACB0 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:102
                                    36        46        56        66        76        86        96       106       116       126  
           DNAB_ECOLI    27 PPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRE 128
               SCOP domains d1b79c_ C: N-terminal domain of DnaB helicase                                                          SCOP domains
               CATH domains 1b79C00 C:26-127 DNAb Helicase; Chain A                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhh....hhh...hhhhhhhhhhhhhhhh.....hhhhhhhhh....hhhh.hhhhhhhhhhh......hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1b79 C  26 PPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRE 127
                                    35        45        55        65        75        85        95       105       115       125  


Chain D from PDB  Type:PROTEIN  Length:103
 aligned with DNAB_ECOLI | P0ACB0 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:103
                                    36        46        56        66        76        86        96       106       116       126   
           DNAB_ECOLI    27 PPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRER 129
               SCOP domains d1b79d_ D: N-terminal domain of DnaB helicase                                                           SCOP domains
               CATH domains 1b79D00 D:26-128 DNAb Helicase; Chain A                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhh....hhh...hhhhhhhhhhhhhhhh.....hhhhhhhhh....hhhh.hhhhhhhhhhh......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1b79 D  26 PPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRER 128
                                    35        45        55        65        75        85        95       105       115       125
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B79)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DNAB_ECOLI | P0ACB0)
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:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    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).
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006269    DNA replication, synthesis of RNA primer    The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
    GO:0006268    DNA unwinding involved in DNA replication    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
    GO:0010212    response to ionizing radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:1990077    primosome complex    Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.

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        DNAB_ECOLI | P0ACB0: 1jwe

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