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(-) Description

Title :  A MEGAVIRIDAE ORFAN GENE ENCODES A NEW NUCLEOTIDYL TRANSFERASE
 
Authors :  A. Lartigue, J. M. Claverie, S. Priet, C. Abergel
Date :  13 Mar 12  (Deposition) - 20 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Mimivirus, Mg662, Transcription Coupled Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ciaccafava, A. Lartigue, P. Mansuelle, S. Jeudy, C. Abergel
A Megaviridae Orphan Gene Encodes A New Nucleotidyl Transferase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L544
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST17
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Organism Common: MIMIVIRUS
    Organism Scientific: ACANTHAMOEBA POLYPHAGA MIMIVIRUS
    Organism Taxid: 212035

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:44 , ASP A:46 , MN A:640 , HOH A:2030BINDING SITE FOR RESIDUE MN A 639
2AC2SOFTWAREASP A:44 , ASP A:46 , ASP A:191 , MN A:639 , HOH A:2031 , HOH A:2032BINDING SITE FOR RESIDUE MN A 640
3AC3SOFTWAREPHE A:71 , ASP A:74 , ILE A:77 , HOH A:2042 , HOH A:2045BINDING SITE FOR RESIDUE MG A1360

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:357 -A:358

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1His A:52 -Pro A:53
2Asn A:117 -Val A:118
3Cys A:357 -Cys A:358

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AMQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AMQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4AMQ)

(-) 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:341
 aligned with YL544_MIMIV | Q5UQA5 from UniProtKB/Swiss-Prot  Length:387

    Alignment length:360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361
          YL544_MIMIV     2 RMLIFTYKLERYIKNKILPKILVVPDRDKYQIKGSFRRRIPYITDIDIVNNVHPEYDDTNIYQRIVDLINSFTNDNQIKLIYVICGTDDRFLLTEYSDEEIEKIKILLNPTELVELNNVLSKYQDDLNKKVFYINEIIWDLYKLRWTSSEVLAGKKILRGGIEVSFQDVVKNNSILLLQYFVKIEYYPIGFDIAVRYKPINLITAYQNAAFYQLKLANYSKEYYFMLFPLRFYFKNDPTISKQLEYIIETKFGLYKQLLVRIDSYRTIYESGNLDLDTAKSIIISIIKDIRKLNGIDMNIIDKIQEVSNNSAGQDKIIAWNTLLTQLYTNINKSVNKQSKKYFTRYINIIPKEDRKLCCL 361
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh...hhh.eeeehhhhh......eeeeeee........hhhhhhhhhhhhhh....eeeeeeeeee.hhhh...hhhhhhhhhh....hhhhhh....--------..hhhhhhhhhhhhheeeehhhhhhhheee.hhh.eeehhhhhhh..eeeeeeeee....eeeeeeeee...-----------....hhhhh......hhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4amq A   0 RMLIFTYKLERYIKNKILPKILVVPDRDKYQIKGSFRRRIPYITDIDIVNNVHPEYDDTNIYQRIVDLINSFTNDNQIKLIYVICGTDDRFLLTEYSDEEIEKIKILLNPTELVELNNV--------NKKVFYINEIIWDLYKLRWTSSEVLAGKKILRGGIEVSFQDVVKNNSILLLQYFVKIEYYPIGFDIAVRYKP-----------FYQLKLANYSKEYYFMLFPLRFYFKNDPTISKQLEYIIETKFGLYKQLLVRIDSYRTIYESGNLDLDTAKSIIISIIKDIRKLNGIDMNIIDKIQEVSNNSAGQDKIIAWNTLLTQLYTNINKSVNKQSKKYFTRYINIIPKEDRKLCCL 359
                                     9        19        29        39        49        59        69        79        89        99       109        |-       129       139       149       159       169       179       189        |-         -|      219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
                                                                                                                                                118      127                                                                    198         210
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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  (0, 0)

(no "SCOP Domain" information available for 4AMQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AMQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AMQ)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YL544_MIMIV | Q5UQA5)
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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