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(-) Description

Title :  CRYSTAL STRUCTURE OF 2'-5' RNA LIGASE FROM PYROCOCCUS HORIKOSHII
 
Authors :  M. Yao, H. Morita, A. Okada, I. Tanaka
Date :  27 Apr 04  (Deposition) - 07 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha+Beta, Ligt-Like, Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. G. Gao, M. Yao, A. Okada, I. Tanaka
The Structure Of Pyrococcus Horikoshii 2'-5' Rna Ligase At 1. 94 A Resolution Reveals A Possible Open Form With A Wider Active-Site Cleft
Acta Crystallogr. , Sect. F V. 62 1196 2006
PubMed-ID: 17142895  |  Reference-DOI: 10.1107/S1744309106046616
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH0099
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-26B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0099
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: 2'-5' RNA LIGASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VGJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:81 -Pro A:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VGJ)

(-) Exons   (0, 0)

(no "Exon" information available for 1VGJ)

(-) 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 THPR_PYRHO | O57823 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
           THPR_PYRHO     1 MRAFIAIDVNESVRDSLVRAQDYIGSKEAKIKFVERENLHITLKFLGEITEEQAEEIKNILKKIAEKYKKHEVKVKGIGVFPNPNYIRVIWAGIENDEIIREMAREIEDELAKLGFKKEGNFVAHITLGRVKFVKDKLGLTMKLKELANEDFGSFVVDAIELKKSTLTPKGPIYETLARFELSE 184
               SCOP domains d1vgja_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhh.eeeeeeee..hhhhhhhhhhhhhhhhh....eeeeeeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhhhh...........eeeeeeeeee.hhhhhhhhhhhh...eeeeeee.eeeeeeeeee..eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgj A   1 mRAFIAIDVNESVRDSLVRAQDYIGSKEAKIKFVERENLHITLKFLGEITEEQAEEIKNILKKIAEKYKKHEVKVKGIGVFPNPNYIRVIWAGIENDEIIREmAREIEDELAKLGFKKEGNFVAHITLGRVKFVKDKLGLTmKLKELANEDFGSFVVDAIELKKSTLTPKGPIYETLARFELSE 184
                            |       10        20        30        40        50        60        70        80        90       100  |    110       120       130       140 |     150       160       170       180    
                            |                                                                                                   103-MSE                                142-MSE                                      
                            1-MSE
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  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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VGJ)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (THPR_PYRHO | O57823)
molecular function
    GO:0004113    2',3'-cyclic-nucleotide 3'-phosphodiesterase activity    Catalysis of the reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate.
    GO:0008664    2'-5'-RNA ligase activity    Catalysis of the formation of a phosphodiester bond between the 2'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another.
    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:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.

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    Phe A:81 - Pro A:82   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        THPR_PYRHO | O57823: 1vdx

(-) Related Entries Specified in the PDB File

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