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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS PYROPHOSPHOHYDROLASE BSRPPH BOUND TO A NON-HYDROLYSABLE TRIPHOSPHORYLATED DINUCLEOTIDE RNA (PCP-PGPG) - FIRST GUANOSINE RESIDUE IN GUANOSINE BINDING POCKET
 
Authors :  J. Piton, V. Larue, Y. Thillier, A. Dorleans, O. Pellegrini, I. Li De L Gallay, J. J. Vasseur, F. Debart, C. Tisne, C. Condon
Date :  03 Apr 13  (Deposition) - 08 May 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nudix Hydrolase, Rna Pyrophosphohydrolase, Rpph, Cytosol, Hydrolase, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Piton, V. Larue, Y. Thillier, A. Dorleans, O. Pellegrini, I. Li De La Sierra-Gallay, J. J. Vasseur, F. Debart, C. Tisne, C. Condon
Bacillus Subtilis Rna Deprotection Enzyme Rpph Recognizes Guanosine In The Second Position Of Its Substrates.
Proc. Natl. Acad. Sci. Usa V. 110 8858 2013
PubMed-ID: 23610407  |  Reference-DOI: 10.1073/PNAS.1221510110

(-) Compounds

Molecule 1 - RNA PYROPHOSPHOHYDROLASE
    ChainsA, B
    EC Number3.6.1.55
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    GeneBSU30630, MUTTA, YTKD
    Organism ScientificBACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid224308
    Strain168
    Synonym8-OXO-DGTPASE, 7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE, DGTP PYROPHOSPHOHYDROLASE
 
Molecule 2 - RNA (5'-R(*(GCP)P*G)-3')
    ChainsC
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A C
Biological Unit 2 (1x) B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GCP1Mod. NucleotidePHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GCP1Mod. NucleotidePHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GCP-1Mod. NucleotidePHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:48 , VAL A:120 , LEU A:121 , PHE A:122 , HIS A:123 , GLU A:124 , GLU B:42 , TYR B:48 , LEU B:121 , PHE B:122 , HIS B:123 , HOH B:319 , HOH B:321 , HOH B:398 , HOH B:404BINDING SITE FOR RESIDUE EPE B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JZU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JZU)

(-) Sequences/Alignments

Asymmetric 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee...........eeeeeeee..eeeeeee...eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeee....eeeeeeeeeeeeee........eeeeeee.....hhhhh...hhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzu A   1 MYEFKDYYQNTVQLSFDDQPFSDSPKHVWVICRFGGKWLLTEHEDRGYEFPGGKVEPMECAEEAALREVKEETGARVKSLKYLGQYKVLGKEKVIVKNIYFADIEKLEKQADYFETKGPVLFHELPENLSRNKKFSFIMKDSVLPISLKKLKESGWI 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       

Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee...........eeeeeeee..eeeeeee...eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeee.eeeeeeeeeeee........eeeeeee.....hhhhh...hhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzu B   1 MYEFKDYYQNTVQLSFDDQPFSDSPKHVWVICRFGGKWLLTEHEDRGYEFPGGKVEPMECAEEAALREVKEETGARVKSLKYLGQYKVLIVKNIYFADIEKLEKQADYFETKGPVLFHELPENLSRNKKFSFIMKDSVLPISLKKLKESGW 156
                                    10        20        30        40        50        60        70        80        95       105       115       125       135       145       155 
                                                                                                                   89|                                                             
                                                                                                                    95                                                             

Chain C from PDB  Type:DNA/RNA  Length:2
                                  
                 4jzu C   1 xG   2
                            | 
                            1-GCP

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  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 4JZU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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 Related Entries

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

UniProtKB/Swiss-Prot
        YTKD_BACSU | O350134jzs 4jzt 4jzv

(-) Related Entries Specified in the PDB File

4jzs 4jzt 4jzv