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(-) Description

Title :  2.1 A CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA RNASE T (RIBONUCLEASE T)
 
Authors :  H. Zheng, M. Chruszcz, M. Cymborowski, Y. Wang, E. Gorodichtchenskaia T. Skarina, J. Guthrie, A. Savchenko, A. Edwards, A. Joachimiak, W. Mi Midwest Center For Structural Genomics (Mcsg)
Date :  05 Dec 05  (Deposition) - 14 Feb 06  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rnase, Rnt, Rnase T, Ribonuclease T, Trna Hydrolase, Sad, Psi, Mcsg, Protein Structure Initiative, Midwest Center For Structural Genomics, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zuo, H. Zheng, Y. Wang, M. Chruszcz, M. Cymborowski, T. Skarina, A. Savchenko, A. Malhotra, W. Minor
Crystal Structure Of Rnase T, An Exoribonuclease Involved I Trna Maturation And End Turnover.
Structure V. 15 417 2007
PubMed-ID: 17437714  |  Reference-DOI: 10.1016/J.STR.2007.02.004

(-) Compounds

Molecule 1 - RIBONUCLEASE T
    Atcc: 15692
    Chains: A, B
    EC Number: 3.1.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11
    Expression System Strain: BL21-GOLD MAGIC (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNT, PA3528
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: EXORIBONUCLEASE T, RNASE T

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:35 , ASP B:137 , HOH B:1084 , HOH B:1095 , HOH B:1109 , HOH B:1119 , HOH B:1120BINDING SITE FOR RESIDUE MG B 1001
2AC2SOFTWAREASP A:35 , HOH A:2048 , HOH A:2098 , HOH A:2099 , HOH A:2100 , HOH A:2103BINDING SITE FOR RESIDUE MG A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F96)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F96)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F96)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F96)

(-) Exons   (0, 0)

(no "Exon" information available for 2F96)

(-) 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:202
 aligned with RNT_PSEAE | Q9HY82 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:202
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218  
            RNT_PSEAE    19 RHPMARRFRGYLPVVVDVETGGFNSATDALLEIAATTVGMDEKGFLFPEHTYFFRIEPFEGANIEPAALEFTGIKLDHPLRMAVQEEAALTEIFRGIRKALKANGCKRAILVGHNSSFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQAAGMEFDNREAHSARYDTEKTAELFCGIVNRWKEMGGWM 220
               SCOP domains d2f96a1 A:19-220 Ribonuclease T                                                                                                                                                                            SCOP domains
               CATH domains 2f96A00 A:19-219  [code=3.30.420.10, no name defined]                                                                                                                                                    - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...eeeeeeeeee.........eeeeeeeeeee.....eee..eeeee..........hhhhhhh.............hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhh...........eeehhhhhhhhh....hhhhhhh............hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f96 A  19 RHPmARRFRGYLPVVVDVETGGFNSATDALLEIAATTVGmDEKGFLFPEHTYFFRIEPFEGANIEPAALEFTGIKLDHPLRmAVQEEAALTEIFRGIRKALKANGCKRAILVGHNSSFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQAAGmEFDNREAHSARYDTEKTAELFCGIVNRWKEmGGWm 220
                               |    28        38        48        58        68        78        88        98 |     108       118       128       138       148       158       168       178      |188       198       208       218 |
                               |                                  58-MSE                                   100-MSE                                                                              185-MSE                        216-MSE
                              22-MSE                                                                                                                                                                                               220-MSE


Chain B from PDB  Type:PROTEIN  Length:202
 aligned with RNT_PSEAE | Q9HY82 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:202
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218  
            RNT_PSEAE    19 RHPMARRFRGYLPVVVDVETGGFNSATDALLEIAATTVGMDEKGFLFPEHTYFFRIEPFEGANIEPAALEFTGIKLDHPLRMAVQEEAALTEIFRGIRKALKANGCKRAILVGHNSSFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQAAGMEFDNREAHSARYDTEKTAELFCGIVNRWKEMGGWM 220
               SCOP domains d2f96b_ B: Ribonuclease T                                                                                                                                                                                  SCOP domains
               CATH domains 2f96B00 B:19-219  [code=3.30.420.10, no name defined]                                                                                                                                                    - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...eeeeeeeeee.........eeeeeeeeeee.....eee..eeeee..........hhhhhhh.............hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh...........eeehhhhhhhhh....hhhhhhh............hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f96 B  19 RHPmARRFRGYLPVVVDVETGGFNSATDALLEIAATTVGmDEKGFLFPEHTYFFRIEPFEGANIEPAALEFTGIKLDHPLRmAVQEEAALTEIFRGIRKALKANGCKRAILVGHNSSFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQAAGmEFDNREAHSARYDTEKTAELFCGIVNRWKEmGGWm 220
                               |    28        38        48        58        68        78        88        98 |     108       118       128       138       148       158       168       178      |188       198       208       218 |
                               |                                  58-MSE                                   100-MSE                                                                              185-MSE                        216-MSE
                              22-MSE                                                                                                                                                                                               220-MSE
   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) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F96)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RNT_PSEAE | Q9HY82)
molecular function
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016896    exoribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    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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