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(-) Description

Title :  STRUCTURE OF AN OLIGORIBONUCLEASE (ORN) FROM COXIELLA BURNETII
 
Authors :  J. Cheung, M. C. Franklin, M. Rudolph, M. Cassidy, E. Gary, F. Burshteyn
Date :  09 Sep 11  (Deposition) - 21 Sep 11  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498  |  Reference-DOI: 10.1002/PROT.24841

(-) Compounds

Molecule 1 - OLIGORIBONUCLEASE
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CBU_1235, ORN
    Organism Scientific: COXIELLA BURNETII
    Organism Taxid: 777

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MG2Ligand/IonMAGNESIUM ION
3MN4Ligand/IonMANGANESE (II) ION
4MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , LEU A:13 , GLU A:14 , ASP A:163 , MN A:185 , MG A:186BINDING SITE FOR RESIDUE MN A 184
2AC2SOFTWAREASP A:12 , MN A:184 , MG A:186 , HOH A:217BINDING SITE FOR RESIDUE MN A 185
3AC3SOFTWAREGLU A:14 , MN A:184 , MN A:185 , HOH A:218BINDING SITE FOR RESIDUE MG A 186
4AC4SOFTWAREASP B:12 , LEU B:13 , GLU B:14 , ASP B:163 , MN B:185 , MG B:187BINDING SITE FOR RESIDUE MN B 184
5AC5SOFTWAREASP B:12 , MN B:184 , MG B:187 , HOH B:211 , HOH B:226BINDING SITE FOR RESIDUE MN B 185
6AC6SOFTWAREARG A:143 , GLN A:162 , ARG A:165 , ASP B:5 , ASP B:6BINDING SITE FOR RESIDUE ACT B 186
7AC7SOFTWAREGLU B:14 , MN B:184 , MN B:185 , HOH B:230BINDING SITE FOR RESIDUE MG B 187

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:110 -B:110

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TR8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TR8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TR8)

(-) Exons   (0, 0)

(no "Exon" information available for 3TR8)

(-) 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:184
 aligned with ORN_COXBU | Q83C93 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:184
                               1                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177    
            ORN_COXBU     - ---MDFSDDNLIWLDLEMTGLDPERDRIIEIATIVTNSHLDILAEGPAFAIHQPDKLLTAMDNWNTSHHTASGLLERVKNSSVDEVEAETLTLAFLEKYVSAGKSPLCGNSVCQDRRFLSRYMPRLNQFFHYRHLDVTTLKILAQRWAPQIAAAHIKESQHLALQDIRDSIEELRYYRAHLLNL 181
               SCOP domains d3tr8a_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee.........eeeeeeeee.....eeee...ee...hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........eee..hhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tr8 A  -2 SNAmDFSDDNLIWLDLEmTGLDPERDRIIEIATIVTNSHLDILAEGPAFAIHQPDKLLTAmDNWNTSHHTASGLLERVKNSSVDEVEAETLTLAFLEKYVSAGKSPLCGNSVCQDRRFLSRYmPRLNQFFHYRHLDVTTLKILAQRWAPQIAAAHIKESQHLALQDIRDSIEELRYYRAHLLNL 181
                               |     7       |17        27        37        47        57|       67        77        87        97       107       117  |    127       137       147       157       167       177    
                               |            15-MSE                                     58-MSE                                                       120-MSE                                                         
                               1-MSE                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with ORN_COXBU | Q83C93 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:184
                               1                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177    
            ORN_COXBU     - ---MDFSDDNLIWLDLEMTGLDPERDRIIEIATIVTNSHLDILAEGPAFAIHQPDKLLTAMDNWNTSHHTASGLLERVKNSSVDEVEAETLTLAFLEKYVSAGKSPLCGNSVCQDRRFLSRYMPRLNQFFHYRHLDVTTLKILAQRWAPQIAAAHIKESQHLALQDIRDSIEELRYYRAHLLNL 181
               SCOP domains d3tr8b_ B: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee.........eeeeeeeee.....eeee...ee...hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........eee..hhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tr8 B  -2 SNAmDFSDDNLIWLDLEmTGLDPERDRIIEIATIVTNSHLDILAEGPAFAIHQPDKLLTAmDNWNTSHHTASGLLERVKNSSVDEVEAETLTLAFLEKYVSAGKSPLCGNSVCQDRRFLSRYmPRLNQFFHYRHLDVTTLKILAQRWAPQIAAAHIKESQHLALQDIRDSIEELRYYRAHLLNL 181
                               |     7       |17        27        37        47        57|       67        77        87        97       107       117  |    127       137       147       157       167       177    
                               1-MSE        15-MSE                                     58-MSE                                                       120-MSE
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "CATH Domain" information available for 3TR8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TR8)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ORN_COXBU | Q83C93)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    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.
biological process
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3tr8
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