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(-) Description

Title :  STRUCTURE OF THE AEROPYRUM PERNIX ORC2 PROTEIN (ADP FORM)
 
Authors :  M. R. Singleton, R. Morales, I. Grainge, N. Cook, M. N. Isupov, D. B. Wig
Date :  09 Aug 04  (Deposition) - 05 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Replication, Orc, Cdc6, Dna Replication Initiation, Dna Binding Protein, Aaa+ Atpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Singleton, R. Morales, I. Grainge, N. Cook, M. N. Isupov, D. B. Wigley
Conformational Changes Induced By Nucleotide Binding In Cdc6/Orc From Aeropyrum Pernix
J. Mol. Biol. V. 343 547 2004
PubMed-ID: 15465044  |  Reference-DOI: 10.1016/J.JMB.2004.08.044

(-) Compounds

Molecule 1 - ORIGIN RECOGNITION COMPLEX SUBUNIT 2 ORC2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: K1
    Expression System Taxid: 562
    Fragment: RESIDUES 2-410
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: HYPOTHETICAL PROTEIN APE0152, ORC2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:57 , ARG A:60 , PRO A:213 , ALA A:214 , HOH A:2011BINDING SITE FOR RESIDUE SO4 A 500
2AC2SOFTWAREARG A:240 , HIS A:241 , SER A:282 , GLU A:283BINDING SITE FOR RESIDUE SO4 A 501
3AC3SOFTWARESER B:57 , ARG B:60 , PRO B:213 , ALA B:214 , HOH B:2033 , HOH B:2052BINDING SITE FOR RESIDUE SO4 B 500
4AC4SOFTWAREARG B:240 , HIS B:241 , SER B:282 , GLU B:283BINDING SITE FOR RESIDUE SO4 B 501
5AC5SOFTWARETYR A:19 , LEU A:24 , ARG A:27 , GLY A:62 , ILE A:63 , GLY A:64 , LYS A:65 , THR A:66 , THR A:67 , TYR A:215 , ARG A:227 , ALA A:259 , ARG A:260 , HOH A:2047 , HOH A:2061 , HOH A:2062BINDING SITE FOR RESIDUE ADP A 700
6AC6SOFTWARETYR B:19 , LEU B:24 , ARG B:27 , GLY B:62 , ILE B:63 , GLY B:64 , LYS B:65 , THR B:66 , THR B:67 , TYR B:215 , ARG B:227 , ALA B:259 , ARG B:260 , HOH B:2003 , HOH B:2036BINDING SITE FOR RESIDUE ADP B 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W5S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W5S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W5S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W5S)

(-) Exons   (0, 0)

(no "Exon" information available for 1W5S)

(-) 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:390
 aligned with CDC62_AERPE | Q9YFU8 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:403
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404   
          CDC62_AERPE     5 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPSGRGMRGRTTLFRLAPHLPADRLIEVVDNIIQAKMAS 407
               SCOP domains d1w5sa2 A:7-293 CDC6-like protein APE0152, N-terminal domain                                                                                                                                                                                                                                         d1w5sa1 A:300-409 CDC6-like protein APE0152, C-terminal domain                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh...........hhhhhhhhhhhhhhhhh......eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.eeeeeee.hhhhhh....hhhhhhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh------.......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..eeee..-------..eeee....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w5s A   7 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSEN------THELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPS-------TTLFRLAPHLPADRLIEVVDNIIQAKMAS 409
                                    16        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      |  -   |   306       316       326       336       346       356       366      |  -    |  386       396       406   
                                                                                                                                                                                                                                                                                                                        293    300                                                                      373     381                            


Chain B from PDB  Type:PROTEIN  Length:396
 aligned with CDC62_AERPE | Q9YFU8 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:403
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404   
          CDC62_AERPE     5 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPSGRGMRGRTTLFRLAPHLPADRLIEVVDNIIQAKMAS 407
               SCOP domains d1w5sb2 B:7-293 CDC6-like protein APE0152, N-terminal domain                                                                                                                                                                                                                                   ------d1w5sb1 B:300-409 CDC6-like protein APE0152, C-terminal domain                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh...........hhhhhhhhhhhhhhhhh..ee..eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.eeeeeee.hhhhhh....hhhhhhhhhhhhhhh......eeeeeeeeeeehhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh........hhhhhhhhhhhhhhh..eeee..-------..eeee....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w5s B   7 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPS-------TTLFRLAPHLPADRLIEVVDNIIQAKMAS 409
                                    16        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      |  -    |  386       396       406   
                                                                                                                                                                                                                                                                                                                                                                                                        373     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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1W5S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1W5S)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CDC62_AERPE | Q9YFU8)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        CDC62_AERPE | Q9YFU8: 1w5t

(-) Related Entries Specified in the PDB File

1w5t STRUCTURE OF THE AEROPYRUM PERNIX ORC2 PROTEIN