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(-) Description

Title :  CRYSTAL STRUCTURE OF THE S1 DOMAIN OF RNASE E FROM E. COLI (NATIVE)
 
Authors :  M. Schubert, R. E. Edge, P. Lario, M. A. Cook, N. C. J. Strynadka, G. A. Mackie, L. P. Mcintosh
Date :  09 Mar 04  (Deposition) - 17 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ob-Fold, Rna-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schubert, R. E. Edge, P. Lario, M. A. Cook, N. C. Strynadka, G. A. Mackie, L. P. Mcintosh
Structural Characterization Of The Rnase E S1 Domain And Identification Of Its Oligonucleotide-Binding And Dimerization Interfaces.
J. Mol. Biol. V. 341 37 2004
PubMed-ID: 15312761  |  Reference-DOI: 10.1016/J.JMB.2004.05.061
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE E
    Chains: A, B
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: S1 DOMAIN (RESIDUES 35-125)
    Gene: RNE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RNASE E

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1SMX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S1PS50126 S1 domain profile.RNE_ECOLI39-119
 		  2A:39-119
B:39-119

(-) Exons   (0, 0)

(no "Exon" information available for 1SMX)

(-) Sequences/Alignments

Asymmetric/Biological 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:87
 aligned with RNE_ECOLI | P21513 from UniProtKB/Swiss-Prot  Length:1061

    Alignment length:87
                                    48        58        68        78        88        98       108       118       
            RNE_ECOLI    39 ANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGS 125
               SCOP domains d1smxa_ A: S1-domain of Ribonuclease E                                                  SCOP domains
               CATH domains 1smxA00 A:39-125 Nucleic acid-binding proteins                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhh.eeeee......eeee.hhhhhhhh..........hhhhh.....eeeeeeee........eee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE S1  PDB: A:39-119 UniProt: 39-119                                                ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1smx A  39 ANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGS 125
                                    48        58        68        78        88        98       108       118       


Chain B from PDB  Type:PROTEIN  Length:81
 aligned with RNE_ECOLI | P21513 from UniProtKB/Swiss-Prot  Length:1061

    Alignment length:87
                                    48        58        68        78        88        98       108       118       
            RNE_ECOLI    39 ANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGS 125
               SCOP domains d1smxb_ B: S1-domain of Ribonuclease E                                                  SCOP domains
               CATH domains 1smxB00 B:39-125 Nucleic acid-binding prot      eins                                    CATH domains
           Pfam domains (1) S1-1smxB01 B:39-119                                                              ------ Pfam domains (1)
           Pfam domains (2) S1-1smxB02 B:39-119                                                              ------ Pfam domains (2)
         Sec.struct. author ...eeeeeeeeehhh.eeeee......eeee.hhhhhhhh..------..hhhhhh....eeeeeeee........eee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE S1  PDB: B:39-119 UniProt: 39-119                                                ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1smx B  39 ANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPA------RPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGS 125
                                    48        58        68        78 |      88        98       108       118       
                                                                    80     87
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: OB (224)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RNE_ECOLI | P21513)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0008995    ribonuclease E activity    Catalysis of the cleavage of single-stranded RNA that is monophosphorylated at its 5'-end; cleavage occurs predominantly at 5 nucleotides from the 5'-end and in A + U-rich regions, and is blocked by the presence of a 5'-triphosphate group.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0000967    rRNA 5'-end processing    Any process involved in forming the mature 5' end of an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNE_ECOLI | P21513: 1slj 1sn8 2bx2 2c0b 2c4r 2fym 2vmk 2vrt 3gcm 3gme 3h1c 3h8a 5f6c

(-) Related Entries Specified in the PDB File

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