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(-) Description

Title :  THE CRYSTAL STRUCTURE OF XC847 FROM XANTHOMONAS CAMPESTRIS: A 3-5 OLIGORIBONUCLEASE OF DNAQ FOLD FAMILY WITH A NOVEL OPPOSINGLY-SHIFTED HELIX
 
Authors :  K. H. Chin, C. Y. Yang, C. C. Chou, A. H. J. Wang, S. H. Chou
Date :  12 Mar 06  (Deposition) - 16 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  3'-5' Oligoribonuclease, Orn, Deddh, Xanthomonas Campestris, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Chin, C. Y. Yang, C. C. Chou, A. H. J. Wang, S. H. Chou
The Crystal Structure Of Xc847 From Xanthomonas Campestris: A 3'-5' Oligoribonuclease Of Dnaq Fold Family With A Novel Opposingly Shifted Helix
Proteins V. 65 1036 2006
PubMed-ID: 17029243  |  Reference-DOI: 10.1002/PROT.21148

(-) Compounds

Molecule 1 - OLIGORIBONUCLEASE
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 340
    Strain: PV. CAMPESTRIS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:15 , HOH A:5083 , HOH A:5084 , HOH A:5085 , HOH A:5086BINDING SITE FOR RESIDUE MG A 5082

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:113 -A:113

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
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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:179
 aligned with ORN_XANCP | Q8P8S1 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:179
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177         
            ORN_XANCP     8 NDRLIWIDLEMTGLDTDRDSIIEIATIVTDAQLNVLAEGPELAIAHSLETLEAMDEWNRNQHRRSGLWQRVLDSQVTHAQAEAQTVAFLSEWIRAGASPMCGNSICQDRRFLHRQMSRLERYFHYRNLDVSTIKELARRWAPAVASGFAKSSAHTALSDVRDSIDELRHYRQFMGTLGG 186
               SCOP domains d2gbza_ A: automated matches                                                                                                                                                        SCOP domains
               CATH domains 2gbzA00 A:8-186  [code=3.30.420.10, no name defined]                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.........eeeeeeeeee....eeee...ee...hhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........eee.hhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gbz A   8 NDRLIWIDLEMTGLDTDRDSIIEIATIVTDAQLNVLAEGPELAIAHSLETLEAMDEWNRNQHRRSGLWQRVLDSQVTHAQAEAQTVAFLGEWIRAGASPMCGNSICQDRRFLHRQMSRLERYFHYRNLDVSTIKELARRWAPAVASGFAKSSAHTALSDVRDSIDELRHYRQFMGTLGG 186
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177
   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (ORN_XANCP | Q8P8S1)
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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