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(-) Description

Title :  T4 DNA POLYMERASE FRAGMENT (RESIDUES 1-388) AT 110K
 
Authors :  J. Wang, P. Yu, T. C. Lin, W. H. Konigsberg, T. A. Steitz
Date :  16 Feb 96  (Deposition) - 14 Oct 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Exonuclease, Dna-Binding, Nucleotidyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wang, P. Yu, T. C. Lin, W. H. Konigsberg, T. A. Steitz
Crystal Structures Of An Nh2-Terminal Fragment Of T4 Dna Polymerase And Its Complexes With Single-Stranded Dna And With Divalent Metal Ions.
Biochemistry V. 35 8110 1996
PubMed-ID: 8679562  |  Reference-DOI: 10.1021/BI960178R
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1 - 388
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: T4 GP43 N388

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1NOZ)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:41 -A:55
2B:41 -B:55

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NOZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NOZ)

(-) 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:346
 aligned with DPOL_BPT4 | P04415 from UniProtKB/Swiss-Prot  Length:898

    Alignment length:369
                                    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         
            DPOL_BPT4     2 KEFYISIETVGNNIVERYIDENGKERTREVEYLPTMFRHCKEESKYKDIYGKNCAPQKFPSMKDARDWMKRMEDIGLEALGMNDFKLAYISDTYGSEIVYDRKFVRVANCDIEVTGDKFPDPMKAEYEIDAITHYDSIDDRFYVFDLLNSMYGSVSKWDAKLAAKLDCEGGDEVPQEILDRVIYMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNRVKMILGERSMKRFSPIGRVKSKLIQNMYGSKEIYSIDGVSILDYLDLYKKFAFTNLPSFSLESVAQHETKKGKLPYDGPINKLRETNHQRYISYNIIDVESVQAIDKIRGFIDLVLSMSYYAKMPFSGVMSPIKTWDAIIFNSL 370
               SCOP domains d1noza_ A: Exonuclease domain of family B         DNA polymerases                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1nozA01 A:2-106,A:339-367 DNA Polymerase,         chain B, domain 1                                      1nozA02 A:107-338  [code=3.30.420.10, no name defined]                                                                                                                                                                                  1nozA01 A:2-106,A:339-367    --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeee.....eeeeeee.......hhh.--------.............hhhhh...---------.hhhhhhhhhhhh........hhh..eeeeeeee..............eeeeeeee....eeeeeee............hhhhh..hhh......hhhhhheeeeee..hhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhh....hhhh..........------..............hhhhhhhh.........hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1noz A   2 DEFYISIETVGNNIVERYIDENGKERTREVEYLPTMFRHCKE--------GKNCAPQKFPSMKDARDWMKR---------GMNDFKLAYISDTYGSEIVYDRKFVRVANCDIEVTGDKFPDPMKAEYEIDAITHYDSIDDRFYVFDLLNSMYGSVSKWDAKLAAKLDCEGGDEVPQEILDRVIYMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNRVKMILGERSMKRFSPIGRVKSKL------SKEIYSIDGVSILDYLDLYKKFAFTNLPSFSLESVAQHETKKGKLPYDGPINKLRETNHQRYISYNIIDVESVQAIDKIRGFIDLVLSMSYYAKMPFSGVMSPIKTWDAIIFNSL 370
                                    11        21        31        41 |       -|       61        71|        -|       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       | -    |  261       271       281       291       301       311       321       331       341       351       361         
                                                                    43       52                  72        82                                                                                                                                                                    249    256                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:346
 aligned with DPOL_BPT4 | P04415 from UniProtKB/Swiss-Prot  Length:898

    Alignment length:369
                                    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         
            DPOL_BPT4     2 KEFYISIETVGNNIVERYIDENGKERTREVEYLPTMFRHCKEESKYKDIYGKNCAPQKFPSMKDARDWMKRMEDIGLEALGMNDFKLAYISDTYGSEIVYDRKFVRVANCDIEVTGDKFPDPMKAEYEIDAITHYDSIDDRFYVFDLLNSMYGSVSKWDAKLAAKLDCEGGDEVPQEILDRVIYMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNRVKMILGERSMKRFSPIGRVKSKLIQNMYGSKEIYSIDGVSILDYLDLYKKFAFTNLPSFSLESVAQHETKKGKLPYDGPINKLRETNHQRYISYNIIDVESVQAIDKIRGFIDLVLSMSYYAKMPFSGVMSPIKTWDAIIFNSL 370
               SCOP domains d1nozb_ B: Exonuclease domain of family B         DNA polymerases                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1nozB01 B:2-106,B:339-367 DNA Polymerase,         chain B, domain 1                                      1nozB02 B:107-338  [code=3.30.420.10, no name defined]                                                                                                                                                                                  1nozB01 B:2-106,B:339-367    --- CATH domains
           Pfam domains (1) ------------------DNA_pol_B_exo1-1nozB03 B        :20-290                                                                                                                                                                                                                                        ---------------------------------------------------DNA_pol_B-1nozB01 B:342-370   Pfam domains (1)
           Pfam domains (2) ------------------DNA_pol_B_exo1-1nozB04 B        :20-290                                                                                                                                                                                                                                        ---------------------------------------------------DNA_pol_B-1nozB02 B:342-370   Pfam domains (2)
         Sec.struct. author ..eeeeee.....eeeeee.....eeeeee............--------...........hhhhh.....---------.hhhhhhhhhhhh........hhh..eeeeeeee..............eeeeeeee....eeeeeee..............hhh...........hhhhhheeeeee..hhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh.....hhh..........------..........eeeehhhhhhhh.........hhhhhhhhh....................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1noz B   2 DEFYISIETVGNNIVERYIDENGKERTREVEYLPTMFRHCKE--------GKNCAPQKFPSMKDARDWMKR---------GMNDFKLAYISDTYGSEIVYDRKFVRVANCDIEVTGDKFPDPMKAEYEIDAITHYDSIDDRFYVFDLLNSMYGSVSKWDAKLAAKLDCEGGDEVPQEILDRVIYMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNRVKMILGERSMKRFSPIGRVKSKL------SKEIYSIDGVSILDYLDLYKKFAFTNLPSFSLESVAQHETKKGKLPYDGPINKLRETNHQRYISYNIIDVESVQAIDKIRGFIDLVLSMSYYAKMPFSGVMSPIKTWDAIIFNSL 370
                                    11        21        31        41 |       -|       61        71|        -|       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       | -    |  261       271       281       291       301       311       321       331       341       351       361         
                                                                    43       52                  72        82                                                                                                                                                                    249    256
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: DNA_pol_B-like (44)
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DPOL_BPT4 | P04415)
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:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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: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.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0039693    viral DNA genome replication    The replication of a viral DNA genome.

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 Related Entries

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        DPOL_BPT4 | P04415: 1noy

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