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(-) Description

Title :  SOLUTION STRUCTURE OF RPPH MUTANT E53A FROM ESCHERICHIA COLI
 
Authors :  H. Li, Y. Bi, C. Jin
Date :  19 Jan 09  (Deposition) - 26 Jan 10  (Release) - 26 Jan 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (21x)
Keywords :  Nudix Family, Hydrolase, Magnesium, Manganese, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Li, Y. Bi, C. Jin
Solution Structure Of Rpph Mutant E53A From Escherichia Coli
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA PYROPHOSPHOHYDROLASE
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET21
    Expression System Vector Type: VECTOR
    Fragment: RESIDUES 1-164
    Gene: RPPH, NUDH, YGDP, B2830, JW2798
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: RPPH, (DI)NUCLEOSIDE POLYPHOSPHATE HYDROLASE, AP5A PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  
NMR Structure (21x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2KDW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 22)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21Lys A:89 -Pro A:90
21Thr A:162 -Pro A:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.RPPH_ECOLI6-149  1A:6-149
2NUDIX_BOXPS00893 Nudix box signature.RPPH_ECOLI38-59  1A:38-59

(-) Exons   (0, 0)

(no "Exon" information available for 2KDW)

(-) 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:164
 aligned with RPPH_ECOLI | P0A776 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           RPPH_ECOLI     1 MIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQAMYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKWFLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMKEFASVVMSLQENTPK 164
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee...ee..eee.....ee...ee.....hhhhhhhhhhhhhhh.....eeeeee....eeee...............eeeeeeeeeee................eeee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----NUDIX  PDB: A:6-149 UniProt: 6-149                                                                                                              --------------- PROSITE (1)
                PROSITE (2) -------------------------------------NUDIX_BOX  PDB: A:38-5--------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kdw A   1 MIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQAMYRALFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKWFLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMKEFASVVMSLQENTPK 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   Legend:   → Mismatch (orange background)
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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 2KDW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (RPPH_ECOLI | P0A776)
molecular function
    GO:0034353    RNA pyrophosphohydrolase activity    Catalysis of the removal of a 5' terminal pyrophosphate from the 5'-triphosphate end of an RNA, leaving a 5'-monophosphate end.
    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:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0050779    RNA destabilization    Any process that decreases the stability of an RNA molecule, making it more vulnerable to degradative processes.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Sites
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  Cis Peptide Bonds
    Lys A:89 - Pro A:90   [ RasMol ]  
    Thr A:162 - Pro A:163   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPPH_ECOLI | P0A776: 2kdv 4s2v 4s2w 4s2x 4s2y

(-) Related Entries Specified in the PDB File

2kdv RPPH, WILD FORM RELATED ID: 16125 RELATED DB: BMRB