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(-) Description

Title :  CRYSTAL STRUCTURE OF DNA REPLICATION INITIATION FACTOR
 
Authors :  J. P. Erzberger, M. M. Pirruccello, J. M. Berger
Date :  21 Mar 02  (Deposition) - 25 Sep 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Aaa+, Helix-Turn-Helix, Nucleotide-Binding, Dna Binding, Replication Initiation, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Erzberger, M. M. Pirruccello, J. M. Berger
The Structure Of Bacterial Dnaa: Implications For General Mechanisms Underlying Dna Replication Initiation
Embo J. V. 21 4763 2002
PubMed-ID: 12234917  |  Reference-DOI: 10.1093/EMBOJ/CDF496

(-) Compounds

Molecule 1 - CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSV272
    Expression System Strain: BL21 RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 76-399
    Gene: DNAA
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:9 , HOH A:31 , HOH A:38 , HOH A:45 , THR A:126 , ADP A:400BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREHOH A:20 , HOH A:22 , HOH A:31 , HOH A:38 , HOH A:39 , ASN A:87 , PHE A:88 , ILE A:89 , ASN A:94 , GLY A:122 , THR A:123 , GLY A:124 , LYS A:125 , THR A:126 , HIS A:127 , ILE A:249 , VAL A:276 , MG A:401BINDING SITE FOR RESIDUE ADP A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L8Q)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:113 -Pro A:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L8Q)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNAAPS01008 DnaA protein signature.DNAA_AQUAE354-373  1A:354-373

(-) Exons   (0, 0)

(no "Exon" information available for 1L8Q)

(-) 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:321
 aligned with DNAA_AQUAE | O66659 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:323
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396   
           DNAA_AQUAE    77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDKRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKKKDRKFKHLVGFLEKQAFDKIC 399
               SCOP domains d1l8qa2 A:77-289 Chromosomal replication initiation factor DnaA                                                                                                                                                      d1l8qa1 A:290-399 Chromosomal replication initiation factor DnaA C-terminal domain IV                          SCOP domains
               CATH domains 1l8qA01 A:77-241 P-loop containing nucleotide triphosphate hydrolases                                                                                                1l8qA02 A:242-290                                1l8qA03 A:291-399  [code=1.10.1750.10, no name defined]                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhh.hhhhhhhhhhhhhhhhhh..eeeeee..hhhhh...hhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhh..--.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNAA  PDB: A:354-373-------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l8q A  77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAmVEHLKKGTINEFRNmYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLmQIVEFVANYYAVKVEDILSDKRNKRTSEARKIAmYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKK--RKFKHLVGFLEKQAFDKIC 399
                                    86        96       106       116       126       136       146       156       166   |   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336   |   346       356       366       376 |  |  386       396   
                                                                                                        155-MSE        170-MSE                                                                                                                                 306-MSE                           340-MSE                               378  |                  
                                                                                                                                                                                                                                                                                                                                          381
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1L8Q)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DNAA_AQUAE | O66659)
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:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
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:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DNAA_AQUAE | O66659: 2hcb 3r8f

(-) Related Entries Specified in the PDB File

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