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(-) Description

Title :  STRUCTURE OF THE RNA PYROPHOSPHOHYDROLASE BDRPPH IN COMPLEX WITH HOLMIUM
 
Authors :  S. A. Messing, S. B. Gabelli, L. M. Amzel
Date :  05 Sep 08  (Deposition) - 24 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nudix, Rna Pyrophosphohydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Messing, S. B. Gabelli, Q. Liu, H. Celesnik, J. G. Belasco, S. A. Pineiro, L. M. Amzel
Structure And Biological Function Of The Rna Pyrophosphohydrolase Bdrpph From Bdellovibrio Bacteriovorus
Structure V. 17 472 2009
PubMed-ID: 19278661  |  Reference-DOI: 10.1016/J.STR.2008.12.022

(-) Compounds

Molecule 1 - PROBABLE PYROPHOSPHOHYDROLASE
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MUTT, BD0714
    Organism Scientific: BDELLOVIBRIO BACTERIOVORUS
    Organism Taxid: 959
    Strain: HD100

 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
1ACT2Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3HO2Ligand/IonHOLMIUM ATOM

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:70 , GLU A:73 , HOH A:1309BINDING SITE FOR RESIDUE HO A 154
2AC2SOFTWARELYS A:31 , LYS A:34 , TRP A:121 , HIS A:129 , HOH A:170 , HOH A:1333BINDING SITE FOR RESIDUE ACT A 1307
3AC3SOFTWAREARG A:30 , ASP A:32 , HOH A:213 , HOH A:1318 , HOH A:1329 , LYS B:128BINDING SITE FOR RESIDUE ACT A 1308
4AC4SOFTWAREGLU B:51 , PHE B:52 , ASN B:136BINDING SITE FOR RESIDUE CL B 154
5AC5SOFTWAREGLU B:70 , GLU B:73 , HOH B:156 , HOH B:157 , HOH B:158BINDING SITE FOR RESIDUE HO B 155

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EEU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EEU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EEU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EEU)

(-) Exons   (0, 0)

(no "Exon" information available for 3EEU)

(-) 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:133
 aligned with Q6MPX4_BDEBA | Q6MPX4 from UniProtKB/TrEMBL  Length:153

    Alignment length:133
                                    27        37        47        57        67        77        87        97       107       117       127       137       147   
         Q6MPX4_BDEBA    18 KGHWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLE 150
               SCOP domains d3eeua_ A: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..eeeeee..........ee..eee.....hhhhhhhhhhhhhhh.eee...eeeeeeeee..eeeeeeeeee.eee.........eeeeehhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eeu A  18 KGHWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLE 150
                                    27        37        47        57        67        77        87        97       107       117       127       137       147   


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with Q6MPX4_BDEBA | Q6MPX4 from UniProtKB/TrEMBL  Length:153

    Alignment length:134
                                    27        37        47        57        67        77        87        97       107       117       127       137       147    
         Q6MPX4_BDEBA    18 KGHWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLEW 151
               SCOP domains d3eeub_ B: automated matc     hes                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee..eeeeee...-----..ee..eee.....hhhhhhhhhhhhhhh.eee...eeeeeeeee..eeeeeeeeee.eee.........eeeeehhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eeu B  18 KGHWIPVVAGFLRKDGKILVGQRPE-----GQWEFPGGKIENGETPEEALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLEW 151
                                    27        37    |    -|       57        67        77        87        97       107       117       127       137       147    
                                                   42    48
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EEU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EEU)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6MPX4_BDEBA | Q6MPX4)
molecular function
    GO:0008413    8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity    Catalysis of the reaction: 8-oxo-7,8-dihydroguanosine triphosphate = 8-oxo-7,8-dihydroguanosine phosphate + diphosphate. 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for transcription.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q6MPX4_BDEBA | Q6MPX4: 3ees 3ef5 3ffu

(-) Related Entries Specified in the PDB File

3ees