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(-) Description

Title :  30-CONFORMER NMR ENSEMBLE OF THE N-TERMINAL, DNA-BINDING DOMAIN OF THE REPLICATION INITIATION PROTEIN FROM A GEMINIVIRUS (TOMATO YELLOW LEAF CURL VIRUS-SARDINIA)
 
Authors :  R. Campos-Olivas, J. M. Louis, D. Clerot, B. Gronenborn, A. M. Gronenborn
Date :  07 Mar 02  (Deposition) - 18 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  A+B Fold, Rbd-Like Fold, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Campos-Olivas, J. M. Louis, D. Clerot, B. Gronenborn, A. M. Gronenborn
The Structure Of A Replication Initiator Unites Diverse Aspects Of Nucleic Acid Metabolism
Proc. Natl. Acad. Sci. Usa V. 99 10310 2002
PubMed-ID: 12130667  |  Reference-DOI: 10.1073/PNAS.152342699
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REP PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN (RESIDUES 4-121), DNA-BINDING DOMAIN
    GeneREP
    Organism ScientificTOMATO YELLOW LEAF CURL SARDINIA VIRUS
    Organism Taxid123735

 Structural Features

(-) Chains, Units

  
NMR Structure (30x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1L5I)

(-) Sites  (0, 0)

(no "Site" information available for 1L5I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L5I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L5I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L5I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L5I)

(-) Exons   (0, 0)

(no "Exon" information available for 1L5I)

(-) Sequences/Alignments

NMR Structure
   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:118
 aligned with REP_TYCSV | P27260 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:118
                                    13        23        33        43        53        63        73        83        93       103       113        
            REP_TYCSV     4 SGRFSIKAKNYFLTYPKCDLTKENALSQITNLQTPTNKLFIKICRELHENGEPHLHILIQFEGKYNCTNQRFFDLVSPTRSAHFHPNIQGAKSSSDVKSYIDKDGDVLEWGTFQIDGR 121
               SCOP domains d1l5ia_ A: DNA-binding domain of REP protein                                                                           SCOP domains
               CATH domains 1l5iA00 A:4-121  [code=3.40.1310.20, no name defined]                                                                  CATH domains
               Pfam domains ---Gemini_AL1-1l5iA01 A:7-120                                                                                        - Pfam domains
         Sec.struct. author ......eeeeeeeee.....hhhhhhhhhhhh.....eeeeeeeeee.....eeeeeeeeeeeeee........ee......ee..eeee....hhhhhhhhh...eeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1l5i A   4 SGRFSIKAKNYFLTYPKCDLTKENALSQITNLQTPTNKLFIKICRELHENGEPHLHILIQFEGKYNCTNQRFFDLVSPTRSAHFHPNIQGAKSSSDVKSYIDKDGDVLEWGTFQIDGR 121
                                    13        23        33        43        53        63        73        83        93       103       113        

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  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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Rep (10)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (REP_TYCSV | P27260)
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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016888    endodeoxyribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

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 Related Entries

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

UniProtKB/Swiss-Prot
        REP_TYCSV | P272601l2m

(-) Related Entries Specified in the PDB File

5297 1H, 13C, AND 15N NMR ASSIGNMENTS. COUPLING CONSTANTS HNHA.
1l2m MINIMIZED AVERAGE STRUCTURE