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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRNA PROCESSING ENZYME RNASE PH FROM PSEUDOMONAS AERUGINOSA
 
Authors :  J. M. Choi, E. Y. Park, J. H. Kim, S. K. Chang, Y. Cho
Date :  15 Oct 03  (Deposition) - 17 Feb 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Beta-Alpha-Beta-Alpha Fold, Hexamer, Phosphate Bound, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Choi, E. Y. Park, J. H. Kim, S. K. Chang, Y. Cho
Probing The Functional Importance Of The Hexameric Ring Structure Of Rnase Ph
J. Biol. Chem. V. 279 755 2004
PubMed-ID: 14573594  |  Reference-DOI: 10.1074/JBC.M309628200

(-) Compounds

Molecule 1 - RIBONUCLEASE PH
    Chains: A
    EC Number: 2.7.7.56
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPH
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: RNASE PH, TRNA NUCLEOTIDYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 78)
No.NameCountTypeFull Name
1MSE36Mod. Amino AcidSELENOMETHIONINE
2NHE6Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3SO436Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:81 , LYS A:83BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWARELYS A:37 , NHE A:2854 , HOH A:2888 , HOH A:2959BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREARG A:87 , GLY A:125 , THR A:126 , ARG A:127 , HOH A:2966 , HOH A:3057BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWAREARG A:81 , GLY A:85 , GLY A:86 , HOH A:2904 , HOH A:2993 , HOH A:2997BINDING SITE FOR RESIDUE SO4 A 1004
5AC5SOFTWARESER A:5 , ARG A:13 , PRO A:14 , GLY A:34 , HOH A:2859 , HOH A:2871BINDING SITE FOR RESIDUE SO4 A 1005
6AC6SOFTWARELYS A:23 , ASP A:35 , HOH A:2918 , HOH A:2972 , HOH A:3051BINDING SITE FOR RESIDUE SO4 A 1006
7AC7SOFTWARETHR A:18 , TYR A:21 , SO4 A:1002 , HOH A:2860 , HOH A:2915 , HOH A:2927 , HOH A:2975BINDING SITE FOR RESIDUE NHE A 2854

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R6L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R6L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R6L)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PHPS01277 Ribonuclease PH signature.RNPH_PSEAE117-129  1A:117-129
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PHPS01277 Ribonuclease PH signature.RNPH_PSEAE117-129  6A:117-129

(-) Exons   (0, 0)

(no "Exon" information available for 1R6L)

(-) 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    
   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:236
 aligned with RNPH_PSEAE | P50597 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
           RNPH_PSEAE     1 MNRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALAE 239
               SCOP domains d1r6la1 A:1-151 Ribonuclease PH, domain 1                                                                                                              d1r6la2 A:152-239 Ribonuclease PH, domain 2                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------RNase_PH-1r6lA01 A:11-143                                                                                                            --------------RNase_PH_C-1r6lA02 A:158-225                                        -------------- Pfam domains
         Sec.struct. author ..............eeee........eeeeeee..eeeeeeeeeee.......---..eeeeeeee..........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee..eeee..hhhhhhhh.eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_-------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r6l A   1 mNRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLK---QGWLTAEYGmLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQmVAAVSVGIYQGVPVLDLDYLEDSAAETDLNVVmTDAGGFIEVQGTAEGAPFRPAELNAmLELAQQGmQELFELQRAALAE 239
                            |       10        20        30        40        50  |   | 60     |  70        80        90       100       110       120       130       140       150       160       170       180       190 |     200       210       220     | 230         
                            |                                                  53  57       66-MSE                                                                                      159-MSE                          192-MSE                   218-MSE 226-MSE         
                            1-MSE
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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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R6L)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: S5 (103)
(-)
Clan: no clan defined [family: RNase_PH_C] (9)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (RNPH_PSEAE | P50597)
molecular function
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0009022    tRNA nucleotidyltransferase activity    Catalysis of the reaction: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate.
    GO:0004549    tRNA-specific ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in tRNA molecules.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0016075    rRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNPH_PSEAE | P50597: 1r6m

(-) Related Entries Specified in the PDB File

1r6m THE SAME PROTEIN COMPLEXED WITH PHOSPHATE