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(-) Description

Title :  SOLUTION STRUCTURES OF RADA INTEIN FROM PYROCOCCUS HORIKOSHII
 
Authors :  J. S. Oeemig, D. Zhou, T. Kajander, A. Wlodawer, H. Iwai
Date :  09 Mar 12  (Deposition) - 16 May 12  (Release) - 25 Jul 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Oeemig, D. Zhou, T. Kajander, A. Wlodawer, H. Iwai
Nmr And Crystal Structures Of The Pyrococcus Horikoshii Rad Intein Guide A Strategy For Engineering A Highly Efficient And Promiscuous Intein.
J. Mol. Biol. V. 421 85 2012
PubMed-ID: 22560994  |  Reference-DOI: 10.1016/J.JMB.2012.04.029

(-) Compounds

Molecule 1 - PHO RADA INTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector: PKRRSF15
    Gene: DNA REPAIR AND RECOMBINATION PROTEIN RADA, PH0263, RADA
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
    Synonym: DNA REPAIR AND RECOMBINATION PROTEIN RADA

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2LQM)

(-) Sites  (0, 0)

(no "Site" information available for 2LQM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LQM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RECA_2PS50162 RecA family profile 1.RADA_PYRHO117-152
325-465		  1-
A:174-174
2INTEIN_N_TERPS50817 Intein N-terminal splicing motif profile.RADA_PYRHO153-249  1A:2-97
3INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.RADA_PYRHO302-325  1A:150-172
NMR Structure * (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RECA_2PS50162 RecA family profile 1.RADA_PYRHO117-152
325-465		  1-
A:174-174
2INTEIN_N_TERPS50817 Intein N-terminal splicing motif profile.RADA_PYRHO153-249  1A:2-97
3INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.RADA_PYRHO302-325  1A:150-172

(-) Exons   (0, 0)

(no "Exon" information available for 2LQM)

(-) 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:174
 aligned with RADA_PYRHO | O58001 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:174
                                   162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322    
           RADA_PYRHO   153 CFARDTEVYYENDTVPHMESIEEMYSKYASMNGELPFDNGYAVPLDNVFVYTLDIASGEIKKTRASYIYREKVEKLIEIKLSSGYSLKVTPSHPVLLFRDGLQWVPAAEVKPGDVVVGVREEVLRRRIISKGELEFHEVSSVRIIDYNNWVYDLVIPETHNFIAPNGLVLHNTQ 326
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...eeeeee..eeeeeehhhhhhhhhhhhh.ee....eeee....eeeeee....eeeeee..eeeeeeeeeeeeeee....eeee....eeeee...eeeee........eeee...hhhhh........eeeeeeeeeeeeeeeeeeee......eee.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) INTEIN_N_TER  PDB: A:2-97 UniProt: 153-249                                                       ---------------------------------------------------------------------------RE PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            - PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2lqm A   1 AFARDTEVYYENDTVPHMESIEEMYSKYASMNGELPFDNGYAVPLDNVFVYTLDIASGEIKKTRASYIYREKVEKLIEIKLSSGYSLKVTPSHPVLLFRDGLQWVPAAEVKPGDVVVGVREEVLRRRIISKGELEFHEVSSVRIIDYNNWVYDLVIPETHNFIAPNGLVLHNAQ 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
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  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 2LQM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LQM)

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (RADA_PYRHO | O58001)
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:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0016539    intein-mediated protein splicing    The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RADA_PYRHO | O58001: 4e2t 4e2u

(-) Related Entries Specified in the PDB File

4e2t RELATED ID: 18320 RELATED DB: BMRB
4e2u