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(-) Description

Title :  STRUCTURE OF E. COLI RPPH BOUND TO RNA AND TWO MAGNESIUM IONS
 
Authors :  N. Vasilyev, A. Serganov
Date :  23 Jan 15  (Deposition) - 11 Feb 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nudix Hydrolase, Rna Pyrophosphohydrolase, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Vasilyev, A. Serganov
Structures Of Rna Complexes With The Escherichia Coli Rna Pyrophosphohydrolase Rpph Unveil The Basis For Specific 5'-End-Dependent Mrna Decay.
J. Biol. Chem. V. 290 9487 2015
PubMed-ID: 25657011  |  Reference-DOI: 10.1074/JBC.M114.634824

(-) Compounds

Molecule 1 - RNA PYROPHOSPHOHYDROLASE
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RPPH, NUDH, YGDP, B2830, JW2798
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: (DI)NUCLEOSIDE POLYPHOSPHATE HYDROLASE, AP5A PYROPHOSPHATASE
 
Molecule 2 - RNA (5'-R(*(APC)*GP*U)-3')
    Chains: B
    Engineered: YES
    Other Details: PREPARED BY IN VITRO TRANSCRIPTION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1APC1Mod. NucleotideDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MG2Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:54 , GLU A:57 , GLU A:58 , GLU A:121 , MG A:202 , SO4 A:204 , HOH A:374 , APC B:1BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREGLN A:38 , GLU A:58 , GLU A:121 , MG A:201 , APC B:1 , HOH B:102BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREASN A:18 , ARG A:19 , GLN A:20 , HOH A:332BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREARG A:9 , GLY A:40 , ARG A:53 , GLU A:54 , GLU A:57 , MG A:201 , HOH A:374 , HOH A:381 , APC B:1BINDING SITE FOR RESIDUE SO4 A 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S2X)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:90 -Pro A:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S2X)

(-) Exons   (0, 0)

(no "Exon" information available for 4S2X)

(-) 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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee....eeeeeee.....ee..eee.....hhhhhhhhhhhhhhh.hhh.eeeeee....eeee.hhhhh......eeeeeeeeeee..hhhhh.........eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s2x A   1 SMIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQAMYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRKPVCIGQKQKWFLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMKEFASVVMSLAA 161
                                    10        20        30        40        50        60        70        80     || 93       103       113       123       133       143       153        
                                                                                                                86|                                                                       
                                                                                                                 90                                                                       


Chain B from PDB  Type:DNA/RNA  Length:3
                                   
                 4s2x B   1 xGU   3
                            |  
                            1-APC
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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  (0, 0)

(no "SCOP Domain" information available for 4S2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S2X)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:90 - Pro A:91   [ RasMol ]  
 

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  4s2x
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  RPPH_ECOLI | P0A776
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  3.6.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPPH_ECOLI | P0A776: 2kdv 2kdw 4s2v 4s2w 4s2y

(-) Related Entries Specified in the PDB File

4s2v 4s2w 4s2y