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(-) Description

Title :  EXOI/SSB-CT COMPLEX
 
Authors :  D. Lu, J. L. Keck
Date :  15 Feb 08  (Deposition) - 08 Jul 08  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Exonuclease, Ssb, Genome Maintenance, Dna Damage, Dna Repair, Hydrolase, Dna Replication, Dna-Binding, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Lu, J. L. Keck
Structural Basis Of Escherichia Coli Single-Stranded Dna-Binding Protein Stimulation Of Exonuclease I.
Proc. Natl. Acad. Sci. Usa V. 105 9169 2008
PubMed-ID: 18591666  |  Reference-DOI: 10.1073/PNAS.0800741105

(-) Compounds

Molecule 1 - EXODEOXYRIBONUCLEASE I
    Chains: A
    EC Number: 3.1.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SBCB, CPEA, XONA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: K12
    Synonym: EXONUCLEASE I, DNA DEOXYRIBOPHOSPHODIESTERASE, DRPASE
 
Molecule 2 - SINGLE-STRANDED DNA-BINDING C-TERMINAL TAIL PEPTIDE
    Chains: B, C
    Engineered: YES
    Other Details: PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE IS FOUND NATURALLY IN E. COLI.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:15 , HOH A:487 , HOH A:492 , HOH A:503 , HOH A:509 , HOH A:512BINDING SITE FOR RESIDUE MG A 483
2AC2SOFTWAREGLU A:318 , ASP A:319BINDING SITE FOR RESIDUE MG A 484

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C94)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C94)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C94)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EXOI_SH3PS51784 Exonuclease I (ExoI) SH3-like domain profile.EX1_ECOLI202-355  1A:202-352
2EXOI_CPS51785 Exonuclease I (ExoI) C-terminal domain profile.EX1_ECOLI358-475  1A:360-475

(-) Exons   (0, 0)

(no "Exon" information available for 3C94)

(-) 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:458
 aligned with EX1_ECOLI | P04995 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              475 
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466        |-
            EX1_ECOLI     7 QQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHSNAHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAEEIV-   -
               SCOP domains d3c94a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3c94A01 A:7-201  [code=3.30.420.10, no name defined]                                                                                                                                               -----------------------------------------------------------------------------------------  ------------------------------------------------------------       --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.........eeeeeeeee..........eeee.........hhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh...hhhhhhhhheeeehhhhhhhhhhhh................hhhhhhhhh.....---..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......eeee.hhhhhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhhh.....--.....eeeee.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhh-------..hhhhh......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EXOI_SH3  PDB: A:202-352 UniProt: 202-355                                                                                                                 --EXOI_C  PDB: A:360-475 UniProt: 358-475                                                                               - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c94 A   7 QQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHS---DAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDL--NAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFA-------SDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYADEIVE 476
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176 |   | 186       196       206       216       226       236       246       256       266       276       286   |  |296       306       316       326       336       346     |   -   |   366       376       386       396       406       416       426       436       446       456       466       476
                                                                                                                                                                                                     178 182                                                                                                         290  |                                                        352     360                                                                                                                    
                                                                                                                                                                                                                                                                                                                        293                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:4
 aligned with A0A0H3GL04_K | A0A0H3GL04 from UniProtKB/TrEMBL  Length:174

    Alignment length:4
         A0A0H3GL04_K   171 DIPF 174
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3c94 B 174 DIPF 177


Chain B from PDB  Type:PROTEIN  Length:4
 aligned with SSB_ECOLI | P0AGE0 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:4
            SSB_ECOLI   175 DIPF 178
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3c94 B 174 DIPF 177


Chain C from PDB  Type:PROTEIN  Length:3
 aligned with A0A0H3GL04_K | A0A0H3GL04 from UniProtKB/TrEMBL  Length:174

    Alignment length:3
         A0A0H3GL04_K   172 IPF 174
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3c94 C 175 IPF 177


Chain C from PDB  Type:PROTEIN  Length:3
 aligned with SSB_ECOLI | P0AGE0 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:3
            SSB_ECOLI   176 IPF 178
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3c94 C 175 IPF 177
   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  (0, 0)

(no "Pfam Domain" information available for 3C94)

(-) Gene Ontology  (28, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EX1_ECOLI | P04995)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    GO:0051575    5'-deoxyribose-5-phosphate lyase activity    Catalysis of the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site in DNA where a DNA-(apurinic or apyrimidinic site) lyase has already cleaved the C-O-P bond 3' to the apurinic or apyrimidinic site.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008852    exodeoxyribonuclease I activity    Catalysis of the degradation of single-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides.
    GO:0004529    exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a DNA molecule.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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).
    GO:0008310    single-stranded DNA 3'-5' exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a single-stranded DNA molecule.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown 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:0000738    DNA catabolic process, exonucleolytic    The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
    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:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    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.

Chain B,C   (SSB_ECOLI | P0AGE0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    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: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:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    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:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0000725    recombinational repair    A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B,C   (A0A0H3GL04_K | A0A0H3GL04)

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  3c94
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  EX1_ECOLI | P04995
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 Related Entries

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

UniProtKB/Swiss-Prot
        EX1_ECOLI | P04995: 1fxx 2qxf 3c95 3hl8 3hp9 4hcb 4hcc 4jrp 4jrq 4js4 4js5
        SSB_ECOLI | P0AGE0: 1eqq 1eyg 1kaw 1qvc 1sru 3sxu 3uf7 4mz9 4z0u
UniProtKB/TrEMBL
        A0A0H3GL04_K | A0A0H3GL04: 4nl8

(-) Related Entries Specified in the PDB File

1fxx APO EXOI
3c95 EXONUCLEASE I (APO)