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(-) Description

Title :  E. COLI RECO COMPLEX WITH SSB C-TERMINUS
 
Authors :  O. Koroleva, M. Ryzhikov, S. Korolev
Date :  06 Jan 11  (Deposition) - 04 May 11  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,E,F
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Keywords :  Dna-Binding Protein, Ob-Fold, Recombination Initation, Recombination Initiation, Ssb, Dna, Recr, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ryzhikov, O. Koroleva, D. Postnov, A. Tran, S. Korolev
Mechanism Of Reco Recruitment To Dna By Single-Stranded Dna Binding Protein.
Nucleic Acids Res. V. 39 6305 2011
PubMed-ID: 21504984  |  Reference-DOI: 10.1093/NAR/GKR199

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN RECO
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RECO
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RECOMBINATION PROTEIN O
 
Molecule 2 - SINGLE-STRANDED DNA-BINDING PROTEIN
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 170-178
    Gene: SSB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABEF
Biological Unit 1 (1x): A E 
Biological Unit 2 (1x):  B F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2GOL1Ligand/IonGLYCEROL
3MLT1Ligand/IonD-MALATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CPS-1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2GOL1Ligand/IonGLYCEROL
3MLT1Ligand/IonD-MALATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2GOL-1Ligand/IonGLYCEROL
3MLT-1Ligand/IonD-MALATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:11 , LYS A:223 , HOH A:313 , HOH A:321 , HOH A:344BINDING SITE FOR RESIDUE MLT A 700
2AC2SOFTWARESER A:16 , THR A:18 , SER A:19 , ARG B:13 , ARG B:33BINDING SITE FOR RESIDUE GOL A 800
3AC3SOFTWAREGLY A:64 , GLU A:65 , VAL A:66 , THR A:163 , HOH A:268 , ARG B:31 , LEU B:90 , SER B:97 , ARG B:98 , LEU B:100 , GLU B:101 , HOH B:245 , HOH B:255 , HOH B:260 , HOH B:265 , HOH B:279 , HOH B:283 , HOH B:310BINDING SITE FOR RESIDUE CPS B 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q8D)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:2 -Gly A:3
2Gly A:125 -Thr A:126
3Ser B:41 -Lys B:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q8D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q8D)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q8D)

(-) 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:231
 aligned with RECO_ECOLI | P0A7H3 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 
           RECO_ECOLI     2 EGWQRAFVLHSRPWSETSLMLDVFTEESGRVRLVAKGARSKRSTLKGALQPFTPLLLRFGGRGEVKTLRSAEAVSLALPLSGITLYSGLYINELLSRVLEYETRFSELFFDYLHCIQSLAGVTGTPEPALRRFELALLGHLGYGVNFTHCAGSGEPVDDTMTYRYREEKGFIASVVIDNKTFTGRQLKALNAREFPDADTLRAAKRFTRMALKPYLGGKPLKSRELFRQFM 232
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.....eeeeeee...eeeeeee........hhhhhh.....eeeeee....eeeeeeeee........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...................eeeee...eeee.......eeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q8d A   2 EGWQRAFVLHSRPWSETSLMLDVFTEESGRVRLVAKGARSKRSTLKGALQPFTPLLLRFGGRGEVKTLRSAEAVSLALPLSGITLYSGLYINELLSRVLEYETRFSELFFDYLHCIQSLAGVTGTPEPALRRFELALLGHLGYGVNFTHCAGSGEPVDDTMTYRYREEKGFIASVVIDNKTFTGRQLKALNAREFPDADTLRAAKRFTRMALKPYLGGKPLKSRELFRQFM 232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with RECO_ECOLI | P0A7H3 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
           RECO_ECOLI     2 EGWQRAFVLHSRPWSETSLMLDVFTEESGRVRLVAKGARSKRSTLKGALQPFTPLLLRFGGRGEVKTLRSAEAVSLALPLSGITLYSGLYINELLSRVLEYETRFSELFFDYLHCIQSLAGVTGTPEPALRRFELALLGHLGYGVNFTHCAGSGEPVDDTMTYRYREEKGFIASVVIDNKTFTGRQLKALNAREFPDADTLRAAKRFTRMALKPYLGGKPLKSRELFRQFMP 233
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) RecO_N-3q8dB01 B:2-78                                                        -RecO_C-3q8dB03 B:80-226                                                                                                                            ------- Pfam domains (1)
           Pfam domains (2) RecO_N-3q8dB02 B:2-78                                                        -RecO_C-3q8dB04 B:80-226                                                                                                                            ------- Pfam domains (2)
         Sec.struct. author ...eeeeeeeeee.....eeeeeee...eeeeeee........hhhhhh.....eeeeee.....eeeeeeee........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...................eeeee...eeee.......eeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q8d B   2 EGWQRAFVLHSRPWSETSLMLDVFTEESGRVRLVAKGARSKRSTLKGALQPFTPLLLRFGGRGEVKTLRSAEAVSLALPLSGITLYSGLYINELLSRVLEYETRFSELFFDYLHCIQSLAGVTGTPEPALRRFELALLGHLGYGVNFTHCAGSGEPVDDTMTYRYREEKGFIASVVIDNKTFTGRQLKALNAREFPDADTLRAAKRFTRMALKPYLGGKPLKSRELFRQFMP 233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  


Chain E from PDB  Type:PROTEIN  Length:3
 aligned with SSB7_ECOLX | P28044 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:3
           SSB7_ECOLX   173 IPF 175
               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
                 3q8d E   7 IPF   9


Chain F from PDB  Type:PROTEIN  Length:3
 aligned with SSB7_ECOLX | P28044 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:3
           SSB7_ECOLX   173 IPF 175
               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
                 3q8d F   7 IPF   9
   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 3Q8D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q8D)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: OB (224)
(-)
Clan: no clan defined [family: RecO_C] (4)

(-) Gene Ontology  (6, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RECO_ECOLI | P0A7H3)
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: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 E,F   (SSB7_ECOLX | P28044)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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.

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