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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  RETROVIRUS-RELATED POL POLYPROTEIN
 
Authors :  A. Dash, K. Beesetti
Date :  12 Jun 02  (Deposition) - 26 Jun 02  (Release) - 26 Jun 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Hydrolase, Transferase, Rna-Directed Dna Polymerase, Nuclease, Endonuclease, Polyprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dash, K. Beesetti
Retrovirus-Related Pol Polyprotein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RETROVIRUS-RELATED POL POLYPROTEIN
    Chains: A
    EC Number: 2.7.7.49
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1M0C)

(-) Sites  (0, 0)

(no "Site" information available for 1M0C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M0C)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Val A:37 -His A:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M0C)

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_INTEGRASEPS50876 Zinc finger integrase-type profile.POL1_CHICK149-190  1A:149-190
2INTEGRASEPS50994 Integrase catalytic domain profile.POL1_CHICK202-246  1A:202-246

(-) Exons   (0, 0)

(no "Exon" information available for 1M0C)

(-) Sequences/Alignments

Theoretical Model
   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:246
 aligned with POL1_CHICK | P10399 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
           POL1_CHICK     1 SAQPVRAFTPWVELLSLLLSKARTSAFRDFGKDLDIVHLPRFFRDSQILPDEILLALHGFGGKLRYAGSLPIFELARPLRVSLRLRVVASPLDGPTVFTDASSSTGQGAVVLTARTAPAAVLHVRSHSDVPGFFTTGNALADQHAGHKVLTVREADLHSTLHLGARALSRTCSIPMAVAREVVQACPHCNSAPALSAGVNPRGIAPLDVWQTDFTLEPRLAPRSWLAVTVDTASTVIVATQHGRAN 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eee........eee.hhhh...eeeeeee.....eeeeee.........hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhh.eee...............................hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------ZF_INTEGRASE  PDB: A:149-190              -----------INTEGRASE  PDB: A:202-246 UniProt: 202-246    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1m0c A   1 SAQPVRAFTPWVELLSLLLSKARTSAFRDFGKDLDIVHLPRFFRDSQILPDEILLALHGFGGKLRYAGSLPIFELARPLRVSLRLRVVASPLDGPTVFTDASSSTGQGAVVLTARTAPAAVLHVRSHSDVPGFFTTGNALADQHAGHKVLTVREADLHSTLHLGARALSRTCSIPMAVAREVVQACPHCNSAPALSAGVNPRGIAPLDVWQTDFTLEPRLAPRSWLAVTVDTASTVIVATQHGRAN 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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 1M0C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1M0C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1M0C)

(-) Gene Ontology  (12, 12)

Theoretical Model(hide GO term definitions)
Chain A   (POL1_CHICK | P10399)
molecular function
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  Sites
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  Cis Peptide Bonds
    Val A:37 - His A:38   [ RasMol ]  
 

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  1m0c
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1M0C)

(-) Related Entries Specified in the PDB File

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1a5x ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3