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Title :  THEORETICAL STRUCTURE OF REPLICATION FACTOR C 36 KDA SUBUNIT
 
Authors :  R. P. K. Surendra, T. Neelima, K. K. Kakarala
Date :  12 Apr 02  (Deposition) - 12 Jun 02  (Release) - 12 Jun 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Activator 1 36 Kda Subunit, Replication Factor C 36 Kda Subunit, A1 36 Kda Subunit, Rf-C 36 Kda Subunit, Rfc36 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. P. K. Surendra, T. Neelima, K. K. Kakarala
Theoretical Structure Of Replication Factor C 36 Kda Subunit
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPLICATION FACTOR C 36 KDA SUBUNIT
    Cellular LocationNUCLEUS
    ChainsA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymACTIVATOR 1 36 KDA SUBUNIT, RFC36

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LFS)

(-) Sites  (0, 0)

(no "Site" information available for 1LFS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Theoretical Model (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018749A13TRFC5_HUMANPolymorphism5745796AA13T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LFS)

(-) Sequences/Alignments

Theoretical Model
   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:340
 aligned with RFC5_HUMAN | P40937 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:340
                                    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
           RFC5_HUMAN     1 METSALKQQEQPAATKIRNLPWVEKYRPQTLNDLISHQDILSTIQKFINEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGIDIIRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYLSKIIPALQSRCTRFRFGPLTPELMVPRLEHVVEEEKVDISEDGMKALVTLSSGDMRRALNILQSTNMAFGKVTEETVYTCTGHPLKSDIANILDWMLNQDFTTAYRNITELKTLKGLALHDILTEIHLFVHRVDFPSSVRIHLLTKMADIEYRLSVGTNEKIQLSSLIAAFQVTRDLIVAEA 340
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhheeeee..hhhhhhhhhhhhhhhhhh.hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhheeeee......hhhhhhhhhhhhhhh.eehhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.eehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lfs A   1 METSALKQQEQPAATKIRNLPWVEKYRPQTLNDLISHQDILSTIQKFINEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGIDIIRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYLSKIIPALQSRCTRFRFGPLTPELMVPRLEHVVEEEKVDISEDGMKALVTLSSGDMRRALNILQSTNMAFGKVTEETVYTCTGHPLKSDIANILDWMLNQDFTTAYRNITELKTLKGLALHDILTEIHLFVHRVDFPSSVRIHLLTKMADIEYRLSVGTNEKIQLSSLIAAFQVTRDLIVAEA 340
                                    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

   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 1LFS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Theoretical Model(hide GO term definitions)
Chain A   (RFC5_HUMAN | P40937)
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:0003689    DNA clamp loader activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their closing around the DNA duplex.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043142    single-stranded DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single-stranded DNA, and it drives another reaction.
biological process
    GO:0042769    DNA damage response, detection of DNA damage    The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    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:0070987    error-free translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
    GO:0042276    error-prone translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
    GO:0006297    nucleotide-excision repair, DNA gap filling    Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
    GO:0033683    nucleotide-excision repair, DNA incision    A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
    GO:0006296    nucleotide-excision repair, DNA incision, 5'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
    GO:1900264    positive regulation of DNA-directed DNA polymerase activity    Any process that activates or increases the frequency, rate or extent of DNA-directed DNA polymerase activity.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0000722    telomere maintenance via recombination    Any recombinational process that contributes to the maintenance of proper telomeric length.
    GO:0006283    transcription-coupled nucleotide-excision repair    The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
    GO:0019985    translesion synthesis    The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
cellular component
    GO:0031390    Ctf18 RFC-like complex    A heptameric complex related to replication factor C, which loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA and plays a vital role in chromosome cohesion. In Saccharomyces the subunits are known as Ctf18p, Rfc2p, Rfc3p, Rfc4p, Rfc5p, Dcc1p, and Ctf8p.
    GO:0005663    DNA replication factor C complex    A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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(-) Related Entries Specified in the PDB File

1iqp 1IQP CHAIN HAS 39% SEQUENCE SIMIALRITY (2E-63) WITH RFCHUAMN