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(-) Description

Title :  CRYSTAL STRUCTURE OF DOMAIN III FROM THE THERMOTOGA MARITIMA REPLICATION INITIATION PROTEIN DNAA
 
Authors :  N. Fujikawa, S. Ozaki, W. Kagawa, S. -Y. Park, T. Katayama, H. Kurumizaka, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Jun 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Aaa+ Atpase, Domain Iii (Atpase Domain), Atp-Binding, Cytoplasm, Dna Replication, Dna-Binding, Nucleotide-Binding, Dna Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ozaki, H. Kawakami, K. Nakamura, N. Fujikawa, W. Kagawa, S. -Y. Park, S. Yokoyama, H. Kurumizaka, T. Katayama
A Common Mechanism For The Atp-Dnaa-Dependent Formation Of Open Complexes At The Replication Origin
J. Biol. Chem. V. 283 8351 2008
PubMed-ID: 18216012  |  Reference-DOI: 10.1074/JBC.M708684200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD18
    Expression System Strain: MC1061
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DNAA
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:144 , ASP A:201 , ASP A:202 , ADP A:501BINDING SITE FOR RESIDUE MG A 500
2AC2SOFTWARETHR B:144 , ASP B:201 , ASP B:202 , ADP B:502BINDING SITE FOR RESIDUE MG B 501
3AC3SOFTWARETHR C:144 , ASP C:201 , ASP C:202 , ADP C:503BINDING SITE FOR RESIDUE MG C 502
4AC4SOFTWARETYR A:102 , ASN A:106 , PHE A:107 , VAL A:108 , ASN A:113 , GLY A:138 , VAL A:139 , GLY A:140 , LEU A:141 , GLY A:142 , LYS A:143 , THR A:144 , HIS A:145 , ILE A:271 , LEU A:299 , ARG A:300 , MG A:500BINDING SITE FOR RESIDUE ADP A 501
5AC5SOFTWARETYR B:102 , ASN B:106 , PHE B:107 , VAL B:108 , ASN B:113 , GLY B:138 , VAL B:139 , GLY B:140 , LEU B:141 , GLY B:142 , LYS B:143 , THR B:144 , HIS B:145 , ILE B:271 , LEU B:299 , ARG B:300 , MG B:501BINDING SITE FOR RESIDUE ADP B 502
6AC6SOFTWARETYR C:102 , ASN C:106 , PHE C:107 , VAL C:108 , ASN C:113 , GLY C:138 , VAL C:139 , GLY C:140 , LEU C:141 , GLY C:142 , LYS C:143 , THR C:144 , HIS C:145 , ILE C:271 , LEU C:299 , ARG C:300 , MG C:502BINDING SITE FOR RESIDUE ADP C 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z4R)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn A:131 -Pro A:132
2Asn B:131 -Pro B:132
3Asn C:131 -Pro C:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z4R)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z4R)

(-) 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:240
 aligned with DNAA_THEMA | P46798 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:240
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
           DNAA_THEMA    96 TPLNPDYTFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKEAILLLKDFIKP 335
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2z4rA01 A:96-263 P-loop containing nucleotide triphosphate hydrolases                                                                                                   2z4rA02 A:264-335  [code=1.10.8.60, no name defined]                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh.....hhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.hhhhhhhhhh....eeeeehhhhhh.hhhhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhh.eeee....hhhhhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z4r A  96 TPLNPDYTFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKEAILLLKDFIKP 335
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with DNAA_THEMA | P46798 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:240
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
           DNAA_THEMA    96 TPLNPDYTFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKEAILLLKDFIKP 335
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2z4rB01 B:96-263 P-loop containing nucleotide triphosphate hydrolases                                                                                                   2z4rB02 B:264-335  [code=1.10.8.60, no name defined]                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh.....hhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.hhhhhhhhhh....eeeeehhhhhh.hhhhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhh.eeee....hhhhhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z4r B  96 TPLNPDYTFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKEAILLLKDFIKP 335
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335


Chain C from PDB  Type:PROTEIN  Length:240
 aligned with DNAA_THEMA | P46798 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:240
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
           DNAA_THEMA    96 TPLNPDYTFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKEAILLLKDFIKP 335
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2z4rC01 C:96-263 P-loop containing nucleotide triphosphate hydrolases                                                                                                   2z4rC02 C:264-335  [code=1.10.8.60, no name defined]                     CATH domains
           Pfam domains (1) --Bac_DnaA-2z4rC01 C:98-316                                                                                                                                                                                                  ------------------- Pfam domains (1)
           Pfam domains (2) --Bac_DnaA-2z4rC02 C:98-316                                                                                                                                                                                                  ------------------- Pfam domains (2)
           Pfam domains (3) --Bac_DnaA-2z4rC03 C:98-316                                                                                                                                                                                                  ------------------- Pfam domains (3)
         Sec.struct. author .......hhhhh.....hhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.hhhhhhhhhh....eeeeehhhhhh.hhhhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhh.eeee....hhhhhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z4r C  96 TPLNPDYTFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKEAILLLKDFIKP 335
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
   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 2Z4R)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DNAA_THEMA | P46798)
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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  2z4r
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  DNAA_THEMA | P46798
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNAA_THEMA | P46798: 2z4s

(-) Related Entries Specified in the PDB File

2z4s THE SAME PROTEIN IN A DIFFERENT SPACE GROUP RELATED ID: TRT001000473.1 RELATED DB: TARGETDB