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(-) Description

Title :  CRYSTAL STRUCTURE OF A HETERODIMER OF CDC6/ORC1 INITIATORS BOUND TO ORIGIN DNA (FROM S. SOLFATARICUS)
 
Authors :  E. L. Cunningham Dueber, J. E. Corn, S. D. Bell, J. M. Berger
Date :  18 Jun 07  (Deposition) - 11 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Winged-Helix Domain, Helix-Turn-Helix, Aaa+ Atpase Domain, Protein-Dna Complex, Double Helix, Replication/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. L. Dueber, J. E. Corn, S. D. Bell, J. M. Berger
Replication Origin Recognition And Deformation By A Heterodimeric Archaeal Orc1 Complex.
Science V. 317 1210 2007
PubMed-ID: 17761879  |  Reference-DOI: 10.1126/SCIENCE.1143690
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELL DIVISION CONTROL PROTEIN 6 HOMOLOG 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSV271
    Expression System Strain: BL21(DE3) CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 15-397
    Gene: CDC6-1
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: CDC6 HOMOLOG 1
 
Molecule 2 - CELL DIVISION CONTROL PROTEIN 6 HOMOLOG 3
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSV271
    Expression System Strain: BL21(DE3) CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 14-394
    Gene: CDC6-3
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: CDC6 HOMOLOG 3
 
Molecule 3 - DNA (33-MER)
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - DNA (33-MER)
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2K1Ligand/IonPOTASSIUM ION
3MG2Ligand/IonMAGNESIUM ION
4SPD2Ligand/IonSPERMIDINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:3 , HOH A:4 , ADP A:8 , THR A:70 , ASP A:146BINDING SITE FOR RESIDUE MG A 6
2AC2SOFTWAREHOH B:1 , ADP B:9 , THR B:69 , ASP B:150 , ASN B:182BINDING SITE FOR RESIDUE MG B 7
3AC3SOFTWAREDA C:20 , DG C:21 , DG C:22 , DT D:12 , DA D:13 , DC D:14BINDING SITE FOR RESIDUE SPD C 34
4AC4SOFTWAREDT C:26 , DT C:27 , DC D:30BINDING SITE FOR RESIDUE SPD C 35
5AC5SOFTWAREHOH A:3 , MG A:6 , PRO A:26 , LEU A:33 , PRO A:34 , THR A:65 , GLY A:66 , THR A:67 , GLY A:68 , LYS A:69 , THR A:70 , ALA A:71 , TYR A:208 , ILE A:216 , ARG A:220 , ALA A:249 , ARG A:250BINDING SITE FOR RESIDUE ADP A 8
6AC6SOFTWAREHOH B:2 , MG B:7 , PRO B:25 , PHE B:29 , ILE B:32 , PRO B:33 , LEU B:63 , GLY B:65 , THR B:66 , GLY B:67 , LYS B:68 , THR B:69 , PHE B:70 , TYR B:207 , TYR B:219 , ALA B:248 , ARG B:249BINDING SITE FOR RESIDUE ADP B 9

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly B:265 -Gly B:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QBY)

(-) 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:366
 aligned with CDC61_SULSO | Q980N4 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:373
                                    26        36        46        56        66        76        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   
          CDC61_SULSO    17 IFINREYLLPDYIPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDTKVKEEYVYMAKEEIERDRVRDIILTLPFHSKLVLMAVVSISSEENVVSTTGAVYETYLNICKKLGVEAVTQRRVSDIINELDMVGILTAKVVNRGRYGKTKEIGLAVDKNIIVRSLIESD 389
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------AAA_22-2qbyA01 A:52-190                                                                                                                    ----------------------------------------------------------------------------------------------------------------Cdc6_C-2     qbyA02 A:303-385                                                      ---- Pfam domains
         Sec.struct. author ...hhhhhh..........hhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh....eeeeeehhhhhhhh...hhhhhhhhhhhh..--.eeeeeee.hhhhhhhh.hhhhhh...eeeee...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh-----.eehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..eeeee.........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qby A  17 IFINREYLLPDYIPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVN--KISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDTKVKEEYVYMAKEEIERDRVRDIILTLPFHSKLVLMAVVSIS-----VSTTGAVYETYLNICKKLGVEAVTQRRVSDIINELDMVGILTAKVVNRGRYGKTKEIGLAVDKNIIVRSLIESD 389
                                    26        36        46        56        66        76        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   
                                                                                                                                                                                    171  |                                                                                                                                     310   316                                                                         
                                                                                                                                                                                       174                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with CDC63_SULSO | Q97WM8 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:368
                                    26        36        46        56        66        76        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        
          CDC63_SULSO    17 KNPKVFIDPLSVFKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLASGGGIIRKEHVDKAIVDYEQERLIEAVKALPFHYKLALRSLIESEDVMSAHKMYTDLCNKFKQKPLSYRRFSDIISELDMFGIVKIRIINRGRAGGVKKYALVEDKEKVLRALNETFEDSIS 384
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------AAA_22-2qbyB01 B:57-190                                                                                                               ------------------------------------------------------------------------------------------------------------Cdc6_C-2qbyB02 B:299-375                                                     --------- Pfam domains
         Sec.struct. author .......hhhhhh.....hhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhhh......eeeeeehhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhh...eeeeee.hhhhhhh..hhhhhhhhhh....eeeeee..........hhhhhhh...eeee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee........eeeeee..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qby B  17 KNPKVFIDPLSVFKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLASGGGIIRKEHVDKAIVDYEQERLIEAVKALPFHYKLALRSLIESEDVMSAHKMYTDLCNKFKQKPLSYRRFSDIISELDMFGIVKIRIINRGRAGGVKKYALVEDKEKVLRALNETFEDSIS 384
                                    26        36        46        56        66        76        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        


Chain C from PDB  Type:DNA  Length:33
                                                                 
                 2qby C   1 AGATTTTCAGATGAAACGTAGGAAATTTACACT  33
                                    10        20        30   


Chain D from PDB  Type:DNA  Length:33
                                                                 
                 2qby D   1 TGTAAATTTCCTACGTTTCATCTGAAAATCTAG  33
                                    10        20        30
   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 2QBY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: Cdc6_C] (1)

(-) Gene Ontology  (4, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDC61_SULSO | Q980N4)
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: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.

Chain B   (CDC63_SULSO | Q97WM8)
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: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.

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  2qby
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  CDC63_SULSO | Q97WM8
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 Related Entries

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