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(-) Description

Title :  HP (2-20) SUBSTITUTION PHE5 TO SER MODIFICATION IN SDS-D25 MICELLES
 
Authors :  K. H. Lee, D. G. Lee, Y. K. Park, K. S. Harm, Y. M. Kim
Date :  27 Apr 03  (Deposition) - 03 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Coil-Helix-Coil, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. H. Lee, D. G. Lee, Y. K. Park, K. S. Harm, Y. M. Kim
Interactions Between Antimicrobial Peptide, Hp(2-20) Derived From Helicobacter Pylori, And Membrain Studied By Nmr Spectroscopy
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 19-MER PEPTIDE FROM 50S RIBOSOMAL PROTEIN L1
    ChainsA
    EngineeredYES
    MutationYES
    Other DetailsTHIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE FOR THIS PEPTIDE WHICH N-TERMINUS OF HELICOBACTER PYLORI RIBOSOMAL PROTEIN L1
    SynonymRIBOSOMAL PROTEIN L1
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:19BINDING SITE FOR RESIDUE NH2 A 20

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P5L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P5L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P5L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P5L)

(-) Exons   (0, 0)

(no "Exon" information available for 1P5L)

(-) 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:20
 aligned with RL1_HELPJ | Q9ZK21 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:20
                                    11        21
             RL1_HELPJ    2 AKKVFKRLEKLFSKIQNDKV 21
               SCOP domains d1p5la_ A:           SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                  1p5l A  1 AKKVSKRLEKLFSKIQNDKx 20
                                    10        20
                                              20-NH2

Chain A from PDB  Type:PROTEIN  Length:20
 aligned with RL1_HELPY | P56029 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:20
                                    11        21
             RL1_HELPY    2 AKKVFKRLEKLFSKIQNDKA 21
               SCOP domains d1p5la_ A:           SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                  1p5l A  1 AKKVSKRLEKLFSKIQNDKx 20
                                    10        20
                                              20-NH2

   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  (1, 1)

NMR Structure
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1P5L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1P5L)

(-) Gene Ontology  (10, 19)

NMR Structure(hide GO term definitions)
Chain A   (RL1_HELPY | P56029)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0015934    large ribosomal subunit    The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain A   (RL1_HELPJ | Q9ZK21)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0015934    large ribosomal subunit    The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RL1_HELPJ | Q9ZK211p0g 1p0j 1p0l 1p0o 1p5k
        RL1_HELPY | P560291ot0 1p0g 1p0j 1p0l 1p0o 1p5k

(-) Related Entries Specified in the PDB File

1p0g HP (2-20)
1p0j HP (2-20) ANALOGUE 1
1p0l HP (2-20) ANALOGUE 2
1p0o HP (2-20) ANALOGUE 3
1p5k HP (2-20) ANALOGUE 4