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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA
 
Authors :  D. J. Hosfield, Y. Guan, B. J. Haas, R. P. Cunningham, J. A. Tainer
Date :  01 Jul 99  (Deposition) - 31 Aug 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Enzyme:Dna Complex, Trinuclear Zn Cluster, Dna Repair Enzyme, Tim Barrel, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Hosfield, Y. Guan, B. J. Haas, R. P. Cunningham, J. A. Tainer
Structure Of The Dna Repair Enzyme Endonuclease Iv And Its Dna Complex: Double-Nucleotide Flipping At Abasic Sites And Three-Metal-Ion Catalysis.
Cell(Cambridge, Mass. ) V. 98 397 1999
PubMed-ID: 10458614  |  Reference-DOI: 10.1016/S0092-8674(00)81968-6

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*TP*CP*C)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*(3DR)P*CP*GP*AP*CP*GP*A)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*G)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - ENDONUCLEASE IV
    Chains: A
    EC Number: 3.1.21.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , HIS A:109 , GLU A:145 , 3DR C:907BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:182 , ASP A:229 , HIS A:231 , DC B:906 , 3DR C:907BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREGLU A:145 , ASP A:179 , HIS A:182 , HIS A:216 , GLU A:261 , 3DR C:907BINDING SITE FOR RESIDUE ZN A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AP_NUCLEASE_F2_4PS51432 AP endonucleases family 2 profile.END4_ECOLI1-280  1A:1-279
2AP_NUCLEASE_F2_1PS00729 AP endonucleases family 2 signature 1.END4_ECOLI69-77  1A:69-77
3AP_NUCLEASE_F2_2PS00730 AP endonucleases family 2 signature 2.END4_ECOLI175-182  1A:175-182
4AP_NUCLEASE_F2_3PS00731 AP endonucleases family 2 signature 3.END4_ECOLI215-231  1A:215-231

(-) Exons   (0, 0)

(no "Exon" information available for 1QUM)

(-) 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:279
 aligned with END4_ECOLI | P0A6C1 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
           END4_ECOLI     1 MKYIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHDAFRWIMQDDRFDGIPLILETINPDIWAEEIAWLKAQQ 279
               SCOP domains d1quma_ A: Endonuclease IV                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1qumA00 A:1-279 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------AP_endonuc_2-1qumA01 A:19-239                                                                                                                                                                                                ---------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhh.hhh.eeee..........hhhhhhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhh.hhh.eeeeeehhhhhhh.....hhhhhhhhhhhhhhhhhhh.eeeeee.ee..........ee........hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AP_NUCLEASE_F2_4  PDB: A:1-279 UniProt: 1-280                                                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------AP_NUCLEA-------------------------------------------------------------------------------------------------AP_NUCLE--------------------------------AP_NUCLEASE_F2_3 ------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qum A   1 MKYIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHDAFRWIMQDDRFDGIPLILETINPDIWAEEIAWLKAQQ 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         


Chain B from PDB  Type:DNA  Length:6
                                      
                 1qum B 901 GCGTCC 906


Chain C from PDB  Type:DNA  Length:7
                                       
                 1qum C 907 xCGACGA 913
                            |      
                          907-3DR  


Chain D from PDB  Type:DNA  Length:13
                                             
                 1qum D 933 TCGTCGGGGACGC 945
                                   942
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (END4_ECOLI | P0A6C1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003906    DNA-(apurinic or apyrimidinic site) lyase activity    Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
    GO:0008833    deoxyribonuclease IV (phage-T4-induced) activity    Catalysis of the endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.
    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:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0000726    non-recombinational repair    A DNA repair process in which that does not require the exchange of genetic material between the broken DNA molecule and a homologous region of DNA.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        END4_ECOLI | P0A6C1: 1qtw 2nq9 2nqh 2nqj 4k1g

(-) Related Entries Specified in the PDB File

1qtw CONTAINS THE HIGH RESOLUTION CRYSTAL STRUCTURE OF ENDOIV WITHOUT BOUND DNA