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(-) Description

Title :  CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL
 
Authors :  H. J. Zuccola, D. J. Filman, D. M. Coen, J. M. Hogle
Date :  14 Dec 99  (Deposition) - 15 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Herpes Simplex Virus, Dna Synthesis, Sliding Clamps, Pcna, Processivity, Dna Binding Protein/Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Zuccola, D. J. Filman, D. M. Coen, J. M. Hogle
The Crystal Structure Of An Unusual Processivity Factor, Herpes Simplex Virus Ul42, Bound To The C Terminus Of Its Cognate Polymerase.
Mol. Cell V. 5 267 2000
PubMed-ID: 10882068  |  Reference-DOI: 10.1016/S1097-2765(00)80422-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE PROCESSIVITY FACTOR
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN
    Organism Common: HERPES SIMPLEX VIRUS TYPE 1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Synonym: DNA-BINDING PROTEIN UL42
 
Molecule 2 - DNA POLYMERASE
    Chains: B, D, F, H
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Taxid: 562
    Fragment: C-TERMINAL 36 AMINO ACIDS
    Organism Common: HERPES SIMPLEX VIRUS TYPE 1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1DML)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:131 -Pro A:132
2Ala C:131 -Pro C:132
3Ala E:131 -Pro E:132
4Ala G:131 -Pro G:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DML)

(-) 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:267
 aligned with PAP_HHV11 | P10226 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:291
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318 
           PAP_HHV11     29 APCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLPLEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKRELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTSTQVQILSNALTKAGQAAANAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK  319
               SCOP domains d1dmla1 A:29-169 UL42                                                                                                                        d1dmla2 A:170-319 UL42                                                                                                                                 SCOP domains
               CATH domains 1dmlA00 A:29-319  [code=3.70.10.10, no name defined]                                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhhhh......eeeee..eeeeeeee..eeeeeeee.hhh.eee.....eeee.eee..ee............eeeeeeeee......eeeeeeee.............eeeee.....eeee......eeeeehhhhhhhhhhhh.......eeeee....eeeee....eeeee.....------------------------.....eee.....eeeee...hhhhhhhhh....eeeeee......eeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dml A   29 APCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLPLEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKRELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEG------------------------NAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK  319
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        |-         -         -   |   258       268       278       288       298       308       318 
                                                                                                                                                                                                                                227                      252                                                                   


Chain B from PDB  Type:PROTEIN  Length:36
 aligned with DPOL_HHV1A | P07917 from UniProtKB/Swiss-Prot  Length:1235

    Alignment length:36
                                  1209      1219      1229      
          DPOL_HHV1A   1200 DDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA 1235
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                1dml B 1200 DDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA 1235
                                  1209      1219      1229      


Chain C from PDB  Type:PROTEIN  Length:272
 aligned with PAP_HHV11 | P10226 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:291
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318 
           PAP_HHV11     29 APCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLPLEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKRELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTSTQVQILSNALTKAGQAAANAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK  319
               SCOP domains d1dmlc1 C:29-169 UL42                                                                                                                        d1dmlc2 C:170-319 UL42                                                                                                                                 SCOP domains
               CATH domains 1dmlC00 C:29-319  [code=3.70.10.10, no name defined]                                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhhhh......eeeee..eeeeeeee..eeeeeeee.hhh.eee.....eeee.eee..ee............eeeeeeeee......eeeeeeee.............eeeee.....eeee......eeeeehhhhhhhhhhhh.......eeeee....eeeeee..eeeeee.....-------------------hhhhhhhh..eee.....eeeee...hhhhhhhhh....eeeeee......eeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dml C   29 APCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLPLEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKRELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEG-------------------GQAAANAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK  319
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        |-         -       248       258       268       278       288       298       308       318 
                                                                                                                                                                                                                                227                 247                                                                        


Chain D from PDB  Type:PROTEIN  Length:36
 aligned with DPOL_HHV1A | P07917 from UniProtKB/Swiss-Prot  Length:1235

    Alignment length:36
                                  1209      1219      1229      
          DPOL_HHV1A   1200 DDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA 1235
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                1dml D 1200 DDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA 1235
                                  1209      1219      1229      


Chain E from PDB  Type:PROTEIN  Length:275
 aligned with PAP_HHV11 | P10226 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:292
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317  
           PAP_HHV11     28 GAPCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLPLEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKRELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTSTQVQILSNALTKAGQAAANAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK  319
               SCOP domains d1dmle1 E:28-169 UL42                                                                                                                         d1dmle2 E:170-319 UL42                                                                                                                                 SCOP domains
               CATH domains 1dmlE00 E:28-319  [code=3.70.10.10, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhhhh.........eeeee..eeeeeeee..eeeeeeee.hhh.eee.....eeee.........hhhhh........eeeeeee......eeeeeeeeee...eeee.hhhheeee......eee......eeee.hhhhhhhhhhh........eeeee....eeeeee..eeeeeeeee.hhhhhhhh-----------------...eeeee.....eeeee...hhhhhhhhh....eeeeee......eeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dml E   28 GAPCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLPLEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKRELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTST-----------------NAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK  319
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227      |  -         -    |  257       267       277       287       297       307       317  
                                                                                                                                                                                                                                        234               252                                                                   


Chain F from PDB  Type:PROTEIN  Length:36
 aligned with DPOL_HHV1A | P07917 from UniProtKB/Swiss-Prot  Length:1235

    Alignment length:36
                                  1209      1219      1229      
          DPOL_HHV1A   1200 DDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA 1235
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh..eee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                1dml F 1200 DDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA 1235
                                  1209      1219      1229      


Chain G from PDB  Type:PROTEIN  Length:275
 aligned with PAP_HHV11 | P10226 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:292
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317  
           PAP_HHV11     28 GAPCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLPLEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKRELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTSTQVQILSNALTKAGQAAANAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK  319
               SCOP domains d1dmlg1 G:28-169 UL42                                                                                                                         d1dmlg2 G:170-319 UL42                                                                                                                                 SCOP domains
               CATH domains 1dmlG00 G:28-319  [code=3.70.10.10, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhhhh.........eeeee..eeeeeeee..eeeeeeee.hhh.eee.....eeee.........hhhhh........eeeeeee......eeeeeeeee.....eee.hhhheeee......eee......eeee.hhhhhhhhhhh........eeeee....eeeeee..eeeeeeeee.hhhhhhhh-----------------...eeeee.....eeeee...hhhhhhhhh....eeeeee......eeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dml G   28 GAPCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLPLEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKRELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTST-----------------NAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK  319
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227      |  -         -    |  257       267       277       287       297       307       317  
                                                                                                                                                                                                                                        234               252                                                                   


Chain H from PDB  Type:PROTEIN  Length:36
 aligned with DPOL_HHV1A | P07917 from UniProtKB/Swiss-Prot  Length:1235

    Alignment length:36
                                  1209      1219      1229      
          DPOL_HHV1A   1200 DDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA 1235
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh..eee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                1dml H 1200 DDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA 1235
                                  1209      1219      1229
   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  (1, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Fold: DNA clamp (88)
(-)
Superfamily: DNA clamp (88)
(-)
Family: DNA polymerase processivity factor (40)
(-)
Protein domain: UL42 (1)
(-)
Human herpesvirus type 1 [TaxId: 10298] (1)
1ad1dmla1A:29-169
1bd1dmla2A:170-319
1cd1dmlc1C:29-169
1dd1dmlc2C:170-319
1ed1dmle1E:28-169
1fd1dmle2E:170-319
1gd1dmlg1G:28-169
1hd1dmlg2G:170-319

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (PAP_HHV11 | P10226)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0039686    bidirectional double-stranded viral DNA replication    A viral DNA replication process where replication occurs in both directions from the starting point. This creates two replication forks, moving in opposite directions.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Chain B,D,F,H   (DPOL_HHV1A | P07917)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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: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: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:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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  Cis Peptide Bonds
    Ala A:131 - Pro A:132   [ RasMol ]  
    Ala C:131 - Pro C:132   [ RasMol ]  
    Ala E:131 - Pro E:132   [ RasMol ]  
    Ala G:131 - Pro G:132   [ RasMol ]  
 
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  1dml
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  DPOL_HHV1A | P07917
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  PAP_HHV11 | P10226
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  2.7.7.7
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

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1b8h BACTERIOPHAGE RB69 PROCESSIVITY FACTOR WITH BOUND PEPTIDE
1plq PROCESSIVITY FACTOR OF POL DELTA