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(-) Description

Title :  STRUCTURE OF THE RNA PYROPHOSPHOHYDROLASE BDRPPH IN COMPLEX WITH GTP AND MAGNESIUM
 
Authors :  S. A. Messing, S. B. Gabelli, L. M. Amzel
Date :  04 Dec 08  (Deposition) - 24 Mar 09  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
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
(for further references see the PDB file header)

(-) 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: BD0714, MUTT
    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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL B:24 , ARG B:40 , ASN B:44 , LEU B:46 , GLU B:51 , PHE B:52 , GLY B:54 , GLY B:55 , LYS B:56 , GLU B:70 , GLU B:74 , ILE B:97 , ILE B:99 , PRO B:133 , ASN B:136 , MG B:154 , MG B:155 , MG B:156 , HOH B:157 , HOH B:158 , HOH B:159 , HOH B:161 , HOH B:162 , HOH B:163BINDING SITE FOR RESIDUE GTP B4032
2AC2SOFTWAREVAL A:24 , ARG A:40 , ASN A:44 , LEU A:46 , GLU A:51 , PHE A:52 , GLY A:54 , GLY A:55 , LYS A:56 , GLU A:70 , GLU A:74 , TYR A:92 , ILE A:97 , PRO A:133 , ASN A:136 , MG A:154 , MG A:155 , MG A:156 , HOH A:157 , HOH A:159 , HOH A:161 , HOH A:162 , HOH A:163BINDING SITE FOR RESIDUE GTP A4033
3AC3SOFTWAREGLU A:70 , GLU A:73 , MG A:155 , HOH A:161 , HOH A:162 , HOH A:163 , GTP A:4033BINDING SITE FOR RESIDUE MG A 154
4AC4SOFTWAREGLU A:70 , GLU A:74 , MG A:154 , MG A:156 , HOH A:159 , HOH A:160 , HOH A:161 , GTP A:4033BINDING SITE FOR RESIDUE MG A 155
5AC5SOFTWAREGLY A:54 , GLU A:74 , MG A:155 , HOH A:157 , HOH A:158 , GTP A:4033BINDING SITE FOR RESIDUE MG A 156
6AC6SOFTWAREGLU B:70 , GLU B:73 , MG B:155 , HOH B:161 , HOH B:162 , HOH B:163 , GTP B:4032BINDING SITE FOR RESIDUE MG B 154
7AC7SOFTWAREGLU B:70 , GLU B:73 , GLU B:74 , MG B:154 , MG B:156 , HOH B:159 , HOH B:160 , HOH B:161 , GTP B:4032BINDING SITE FOR RESIDUE MG B 155
8AC8SOFTWAREGLY B:54 , GLU B:74 , MG B:155 , HOH B:157 , HOH B:158 , HOH B:159 , GTP B:4032BINDING SITE FOR RESIDUE MG B 156

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FFU)

(-) 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
                                    28        38        48        58        68        78        88        98       108       118       128       138       148   
         Q6MPX4_BDEBA    19 GHWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLEW 151
               SCOP domains d3ffua_ A: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeee..........ee..eee.....hhhhhhhhhhhhhhh.eee...eeeeeeeee..eeeeeeeeee.eee..........eeeehhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ffu A  19 GHWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLEW 151
                                    28        38        48        58        68        78        88        98       108       118       128       138       148   


Chain B from PDB  Type:PROTEIN  Length:133
 aligned with Q6MPX4_BDEBA | Q6MPX4 from UniProtKB/TrEMBL  Length:153

    Alignment length:133
                                    29        39        49        59        69        79        89        99       109       119       129       139       149   
         Q6MPX4_BDEBA    20 HWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLEWR 152
               SCOP domains d3ffub_ B: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.ee..eeeeee..........ee..eee.....hhhhhhhhhhhhhhh.eee...eeeeeeeee..eeeeeeeee..eee..........eeeehhhhhhhh..hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ffu B  20 HWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPEELKHRNIPEANRKILHKIYKALGLEWR 152
                                    29        39        49        59        69        79        89        99       109       119       129       139       149
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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)

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        Q6MPX4_BDEBA | Q6MPX4: 3ees 3eeu 3ef5

(-) Related Entries Specified in the PDB File

3ees 3eeu 3ef5