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(-) Description

Title :  OTU DOMAIN OF CRIMEAN CONGO HEMORRHAGIC FEVER VIRUS
 
Authors :  M. Akutsu, Y. Ye, S. Virdee, D. Komander
Date :  04 Nov 10  (Deposition) - 02 Feb 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Otu Domain, De-Ubiquitinase, De-Isgylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Akutsu, Y. Ye, S. Virdee, J. W. Chin, D. Komander
Molecular Basis For Ubiquitin And Isg15 Cross-Reactivity In Viral Ovarian Tumor Domains.
Proc. Natl. Acad. Sci. Usa V. 108 2228 2011
PubMed-ID: 21266548  |  Reference-DOI: 10.1073/PNAS.1015287108

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE L
    ChainsA, B
    EC Number3.4.19.12, 2.7.7.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1-217
    GeneL
    Organism CommonCCHFV
    Organism ScientificCRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS STRAIN IBAR10200
    Organism Taxid652961
    StrainNIGERIA/IBAR10200/1970
    SynonymPROTEIN L, LARGE STRUCTURAL PROTEIN, REPLICASE, TRANSCRIPTASE, UBIQUITIN THIOLESTERASE, RNA-DIRECTED RNA POLYMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CSD2Mod. Amino Acid3-SULFINOALANINE
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:125 , HOH A:277 , HOH A:281 , ARG B:70BINDING SITE FOR RESIDUE GOL A 218

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PHU)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OTUPS50802 OTU domain profile.L_CCHFI29-158
 
  2A:29-158
B:29-158
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OTUPS50802 OTU domain profile.L_CCHFI29-158
 
  1A:29-158
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OTUPS50802 OTU domain profile.L_CCHFI29-158
 
  1-
B:29-158

(-) Exons   (0, 0)

(no "Exon" information available for 3PHU)

(-) 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:184
 aligned with L_CCHFI | Q6TQR6 from UniProtKB/Swiss-Prot  Length:3945

    Alignment length:184
                             1                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    
              L_CCHFI     - -MDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREALSLMDRVIAVDQLTS 183
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh...eeee..eeee....hhhhheeee......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhh...eeeeee.....eeeeeee........eeeeee...eeeeeee............hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------OTU  PDB: A:29-158 UniProt: 29-158                                                                                                ------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3phu A   0 PMDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNcFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREALSLMDRVIAVDQLTS 183
                                     9        19        29        39|       49        59        69        79        89        99       109       119       129       139       149       159       169       179    
                                                                   40-CSD                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with L_CCHFI | Q6TQR6 from UniProtKB/Swiss-Prot  Length:3945

    Alignment length:192
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192  
              L_CCHFI     3 FLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREALSLMDRVIAVDQLTSSSSDELQDYED 194
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------------OTU-3phuB01 B:35-152                                                                                                  -----------   ---------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------OTU-3phuB02 B:35-152                                                                                                  -----------   ---------------------------- Pfam domains (2)
         Sec.struct. author hhhhh..eeee..eeee....hhhhheeee......hhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhh...eeeee.---....eeeee........eeeeee...eeeeeee......---...hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------OTU  PDB: B:29-158 UniProt: 29-158                                                                                                ------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3phu B   3 FLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNcFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTV---DEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFET---EALSLMDRVIAVDQLTSSSSDELQDYED 194
                                    12        22        32       |42        52        62        72        82        92       102       112        |-  |    132       142       152       162|   |  172       182       192  
                                                                40-CSD                                                                          121 125                                   163 167                           

   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  (0, 0)

(no "SCOP Domain" information available for 3PHU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (L_CCHFI | Q6TQR6)
molecular function
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    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:0039696    RNA-templated viral transcription    A transcription process that uses viral RNA as a template.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039648    modulation by virus of host protein ubiquitination    Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
    GO:0039689    negative stranded viral RNA replication    A viral genome replication process where the template genome is negative stranded, single stranded RNA ((-)ssRNA).
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039579    suppression by virus of host ISG15 activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host ubiquitin-like protein ISG15 activity. ISG15 is a ubiquitin-like protein that is conjugated to lysine residues on various target proteins. Viruses escape from the antiviral activity of ISG15 by using different mechanisms; the influenza B virus NS1 protein for instance blocks the covalent linkage of ISG15 to its target proteins by directly interacting with ISG15. The papain-like protease from the coronavirus cleaves ISG15 derivatives.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

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 Related Entries

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        L_CCHFI | Q6TQR63phw 3phx 3znh 5v5g 5v5h 5v5i

(-) Related Entries Specified in the PDB File

3phw 3phx