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(-) Description

Title :  CRYSTAL FORM B2
 
Authors :  S. Bailey, W. K. Eliason, T. A. Steitz
Date :  05 Sep 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  5.02
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Helicase, Replication Dnab, Hexameric (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Bailey, W. K. Eliason, T. A. Steitz
Structure Of Hexameric Dnab Helicase And Its Complex With A Domain Of Dnag Primase
Science V. 318 459 2007
PubMed-ID: 17947583  |  Reference-DOI: 10.1126/SCIENCE.1147353
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPLICATIVE HELICASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDNAB
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    SynonymDNAB HELICASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:211 , SER A:213 , VAL A:214 , GLY A:215 , LYS A:216 , THR A:217BINDING SITE FOR RESIDUE SO4 A 500
2AC2SOFTWAREARG B:211 , SER B:213 , VAL B:214 , GLY B:215 , LYS B:216 , THR B:217BINDING SITE FOR RESIDUE SO4 B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R6E)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Arg A:8 -Ile A:9
2Glu A:133 -Asp A:134
3Ser A:198 -Gly A:199
4Gly A:266 -Lys A:267
5Gly A:384 -Ser A:385
6Arg B:8 -Ile B:9
7Glu B:133 -Asp B:134
8Ser B:198 -Gly B:199
9Gly B:266 -Lys B:267
10Gly B:384 -Ser B:385

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R6E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R6E)

(-) Exons   (0, 0)

(no "Exon" information available for 2R6E)

(-) 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:387
 aligned with Q9X4C9_GEOSE | Q9X4C9 from UniProtKB/TrEMBL  Length:454

    Alignment length:434
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437    
         Q9X4C9_GEOSE     8 RIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIEMLHNRDGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNL 441
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.---------------------------------.....hhhhhhhhh......eeeee.....hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh.....eeeeehhhhh.....----.hhhhhhhhhhhhhhhhhhh..eeeee.........---...hhhhhh..hhhhhh.eeeeee....-------..eeeeeeeee.....eeeeeeee....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6e A   8 RIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVS---------------------------------GIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGR----RQQEVSEISRSLKALARELEVPVIALSQLSRSVEQR---RPMMSDIRESGSIEQDADIVAFLYRDDY-------KNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNL 441
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147   |     -         -         -       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  |    337       347       357       367  |   |377       387       397   |     - |     417       427       437    
                                                                                                                                                                         151                               185                                                                                                                                              330  335                                370 374                        401     409                                

Chain B from PDB  Type:PROTEIN  Length:387
 aligned with Q9X4C9_GEOSE | Q9X4C9 from UniProtKB/TrEMBL  Length:454

    Alignment length:434
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437    
         Q9X4C9_GEOSE     8 RIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIEMLHNRDGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNL 441
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -DnaB-2r6eB03 B:9-111                                                                                   ----------------------------------------                                 DnaB_C-2r6eB01 B:185-441                                                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) -DnaB-2r6eB04 B:9-111                                                                                   ----------------------------------------                                 DnaB_C-2r6eB02 B:185-441                                                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh---------------------------------.....hhhhhhhhh......eeeee.....hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh.....eeeeehhhhh.....----.hhhhhhhhhhhhhhhhhhh..eeeee.........---...hhhhhh..hhhhhh.eeeeee....-------..eeeeeeeee.....eeeeeeee....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6e B   8 RIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVS---------------------------------GIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGR----RQQEVSEISRSLKALARELEVPVIALSQLSRSVEQR---RPMMSDIRESGSIEQDADIVAFLYRDDY-------KNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNL 441
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147   |     -         -         -       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  |    337       347       357       367  |   |377       387       397   |     - |     417       427       437    
                                                                                                                                                                         151                               185                                                                                                                                              330  335                                370 374                        401     409                                

   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 2R6E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R6E)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9X4C9_GEOSE | Q9X4C9)
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:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    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.
cellular component
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q9X4C9_GEOSE | Q9X4C92r6a 2r6c 2r6d 4esv 4m4w

(-) Related Entries Specified in the PDB File

2r6a CRYSTAL FORM BH1
2r6c CRYSTAL FORM BH2
2r6d CRYSTAL FORM B1