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(-) Description

Title :  CRYSTAL STRUCTURE OF CDC6P FROM PYROBACULUM AEROPHILUM
 
Authors :  J. Liu, C. L. Smith, D. Deryckere, K. Deangelis, G. S. Martin, J. M. Berger
Date :  22 Aug 00  (Deposition) - 04 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cdc6, Cdc18, Orc1, Aaa Protein, Dna Replication Initation Factor, Cell Cycle Control Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, C. L. Smith, D. Deryckere, K. Deangelis, G. S. Martin, J. M. Berger
Structure And Function Of Cdc6/Cdc18: Implications For Origin Recognition And Checkpoint Control.
Mol. Cell V. 6 637 2000
PubMed-ID: 11030343  |  Reference-DOI: 10.1016/S1097-2765(00)00062-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELL DIVISION CONTROL PROTEIN 6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLASMID PET28B
    Expression System Taxid: 562
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773
    Synonym: CDC6P

 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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/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

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:57 , ADP A:398 , HOH A:403 , HOH A:407 , HOH A:420 , HOH A:426BINDING SITE FOR RESIDUE MG A 390
2AC2SOFTWARETHR B:57 , ADP B:399 , HOH B:415 , HOH B:419 , HOH B:420 , HOH B:421BINDING SITE FOR RESIDUE MG B 391
3AC3SOFTWARETYR A:13 , PRO A:15 , LEU A:18 , PRO A:19 , ARG A:21 , GLY A:53 , THR A:54 , GLY A:55 , LYS A:56 , THR A:57 , VAL A:58 , TYR A:192 , ILE A:200 , ARG A:204 , ALA A:239 , ILE A:243 , MG A:390 , HOH A:407 , HOH A:408 , HOH A:419 , HOH A:420 , HOH A:426 , HOH A:430 , HOH A:453 , HOH A:508BINDING SITE FOR RESIDUE ADP A 398
4AC4SOFTWARETYR B:13 , LEU B:18 , PRO B:19 , ARG B:21 , GLY B:53 , THR B:54 , GLY B:55 , LYS B:56 , THR B:57 , VAL B:58 , TYR B:192 , ILE B:200 , ARG B:204 , ALA B:239 , ILE B:243 , MG B:391 , HOH B:401 , HOH B:404 , HOH B:415 , HOH B:416 , HOH B:419 , HOH B:420 , HOH B:444 , HOH B:474BINDING SITE FOR RESIDUE ADP B 399

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1FNN)

(-) 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:379
 aligned with Q8ZYK1_PYRAE | Q8ZYK1 from UniProtKB/TrEMBL  Length:389

    Alignment length:388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
         Q8ZYK1_PYRAE     2 AIVVDDSVFSPSYVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGERPRVHSQLWSYLNDLREKGIVETRQNKRGEGVRGRTTLISIGTEPLDTLEAVITKLIKEELR 389
               SCOP domains d1fnna2 A:1-276 CDC6, N-domain                                                                                                                                                                                                                                                      d1fnna1 A:277-388 CDC6, C-terminal domain                                                                        SCOP domains
               CATH domains 1fnnA01          1fnnA02 A:18-191 P-loop containing nucleotide triphosphate hydrolases                                                                                                         1fnnA01 A:1-17,A:192-275  [code=1.10.8.60, no name defined]                         1fnnA03 A:276-388 'winged helix' repressor DNA binding domain                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..........hhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh.hhhhhh...eeeeeee..hhhhhh.hhhhhhhhh..eee....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeee.---------.eeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fnn A   1 AIVVDDSVFSPSYVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGERPRVHSQLWSYLNDLREKGIVETRQN---------TTLISIGTEPLDTLEAVITKLIKEELR 388
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 |       - |     370       380        
                                                                                                                                                                                                                                                                                                                                                                                         352       362                          


Chain B from PDB  Type:PROTEIN  Length:379
 aligned with Q8ZYK1_PYRAE | Q8ZYK1 from UniProtKB/TrEMBL  Length:389

    Alignment length:388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
         Q8ZYK1_PYRAE     2 AIVVDDSVFSPSYVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGERPRVHSQLWSYLNDLREKGIVETRQNKRGEGVRGRTTLISIGTEPLDTLEAVITKLIKEELR 389
               SCOP domains d1fnnb2 B:1-276 CDC6, N-domain                                                                                                                                                                                                                                                      d1fnnb1 B:277-388 CDC6, C-terminal domain                                                                        SCOP domains
               CATH domains 1fnnB01          1fnnB02 B:18-191 P-loop containing nucleotide triphosphate hydrolases                                                                                                         1fnnB01 B:1-17,B:192-275  [code=1.10.8.60, no name defined]                         1fnnB03 B:276-387 'winged helix' repressor DNA binding domain                                                   - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..........hhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh.hhhhhh...eeeeeee..hhhhhh.hhhhhhhhh..eee....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeee.---------.eeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fnn B   1 AIVVDDSVFSPSYVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGERPRVHSQLWSYLNDLREKGIVETRQN---------TTLISIGTEPLDTLEAVITKLIKEELR 388
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 |       - |     370       380        
                                                                                                                                                                                                                                                                                                                                                                                         352       362
   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  (3, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8ZYK1_PYRAE | Q8ZYK1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.

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