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(-)Asym./Biol. Unit
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(-) Description

Title :  STRUCTURE OF THE AVRBS3-DNA COMPLEX PROVIDES NEW INSIGHTS INTO THE INITIAL THYMINE-RECOGNITION MECHANISM
 
Authors :  S. Stella, R. Molina, I. Yefimenko, J. Prieto, G. H. Silva, C. Bertonati A. Juillerat, P. Duchateau, G. Montoya
Date :  30 Oct 12  (Deposition) - 28 Aug 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Stella, R. Molina, I. Yefimenko, J. Prieto, G. H. Silva, C. Bertonati, A. Juillerat, P. Duchateau, G. Montoya
Structure Of The Avrbs3-Dna Complex Provides New Insights Into The Initial Thymine-Recognition Mechanism
Acta Crystallogr. , Sect. D V. 69 1707 2013
PubMed-ID: 23999294  |  Reference-DOI: 10.1107/S0907444913016429

(-) Compounds

Molecule 1 - AVRBS3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET24A
    Expression System Vector Type: PLASMID
    Organism Scientific: XANTHOMONAS CAMPESTRIS
    Organism Taxid: 339
    Synonym: AVIRULENCE PROTEIN AVRBS3
 
Molecule 2 - 5'-D(*TP*TP*TP*AP*TP*AP*TP*AP*AP*AP*CP*CP*TP*AP *AP*CP*CP*CP*TP*CP*TP*AP)-3'
    Chains: B
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*AP*GP*AP*GP*GP*GP*TP*TP*AP*GP*GP*TP*TP *TP*AP*TP*AP*TP*AP*AP)-3'
    Chains: C
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2YPF)

(-) Sites  (0, 0)

(no "Site" information available for 2YPF)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YPF)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ala A:201 -Ala A:202
2Ala A:216 -Leu A:217
3Ala A:220 -Thr A:221
4Arg A:236 -Ala A:237
5Pro A:251 -Pro A:252
6Leu A:287 -Asn A:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YPF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YPF)

(-) Exons   (0, 0)

(no "Exon" information available for 2YPF)

(-) 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:675
 aligned with AVRB3_XANEU | P14727 from UniProtKB/Swiss-Prot  Length:1164

    Alignment length:675
                                   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       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856     
         AVRB3_XANEU    187 GFTHAHIVALSQHPAALGTVAVKYQDMIAALPEATHEAIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNSGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNIGGKQALETVQALLPVLCQAHGLTPEQVVAIASNIGGKQALETVQALLPVLCQAHGLTPEQVVAIASNIGGKQALETVQALLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNSGGKQALETVQALLPVLCQAHGLTPEQVVAIASNSGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGRPALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVL  861
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................................hhhhhhh....hhhhhhhhhhh.......hhhhhh...hhhhhhhhhhhh.............hhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhh.....hhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhh.hhhhhh....hhhhhhhhhh..hhhhhhhhhhhh.hhhhhh...hhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhh..hhhhhhhhh.............hhhhhhhhhh....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ypf A  185 AFTHAHIVALSQHPAALATVAVKYQDMIAALPEATHEAIVAVAKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNIGGKQALETVQALLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNIGGKQALETVQALLPVLCQAHGLTPEQVVAIASNIGGKQALETVQALLPVLCQAHGLTPEQVVAIASNIGGKQALETVQALLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNIGGKQALETVQALLPVLCQAHGLTPEQVVAIASNIGGKQALETVQALLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAAGLTPEQVVAIASHDGGKQALETVQRLLPVL  861
                                   195|      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       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856     
                                  193||                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                   195|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                    197                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain A from PDB  Type:PROTEIN  Length:675
 aligned with Q3ZD73_XANCA | Q3ZD73 from UniProtKB/TrEMBL  Length:1321

    Alignment length:831
                                   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       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016 
        Q3ZD73_XANCA    187 GFTHAHIVALSQHPAALGTVAVKYQDMIAALPEATHEAIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPEQVVAIASNNGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASIGGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASNGGGKQALETVQRLLPVLCQAPHCLTPEQVVAIASNIGGKQALETVQALLPVLCQAPHCLTPEQVVAIASNGGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASNGGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASHDGGKQALETVQRLLPVLCQAPHDLTPQQVVAIASNGGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASHDGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASNIGGKQALETVQALLPVLCQAPHCLTPEQVVAIASHDGGKQALETVQALLPVLCQAPHDLTPEQVVAIASNIGGKQALETVQRLLPVLCQAPHDLTREQVVAIASHDGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASNGGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASHDGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASNGGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASHDGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASHDGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASNGGGKQALETVQRLLPVLCQAPHDLTPEQVVAIASNGGGKQALETVQALLPVLCQAPHDLTPEQVVAIASNIGGKQALETVQRLLPVL 1017
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................................hhhhhhh....hhhhhhhhhhh.......hhhhhh...hhhhhhhhhhhh.............hhhhhhhh..hhhhhhhhhhhhhhhhhh.------------------------------------...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh-...hhhhhhhhhh..hhhhhhhhhhhhhhhhhh.-...hhhhhhhhhh..hhhhhhhhhhhhhhhhhh.-...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh------------------------------------hh.hhhhhh......hhhhhhhhhhhhhhhhhh.------------------------------------...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh-...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh------------------------------------...hhhhhhhhh...hhhhhhhhhhhhhhhhhh.-...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh-...hhhhhhhhhh..hhhhhhh.....hhhhhh.-...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh-hh.hhhhh.......hhhhhhhhhhh.hhhhhh.-...hhhhhhhhhh..hhhhhhhhhhhh.hhhhhh-...hhhhhhhhhh..hhhhhhhhhhhhh......-.....hhhhhhhh..hhhhhhhhh............-.hhhhhhhhhh....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ypf A  185 AFTHAHIVALSQHPAALATVAVKYQDMIAALPEATHEAIVAVAKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPEQVVAIASHDGGKQALETVQRLLPVLCQA------------------------------------HGLTPQQVVAIASNGGGKQALETVQRLLPVLCQA-HGLTPEQVVAIASNIGGKQALETVQALLPVLCQA-HGLTPQQVVAIASNGGGKQALETVQRLLPVLCQA-HGLTPEQVVAIASNIGGKQALETVQALLPVLCQA------------------------------------HGLTPEQVVAIASNIGGKQALETVQALLPVLCQA------------------------------------HGLTPEQVVAIASNIGGKQALETVQALLPVLCQA-HGLTPEQVVAIASHDGGKQALETVQRLLPVLCQA------------------------------------HGLTPEQVVAIASHDGGKQALETVQRLLPVLCQA-HGLTPQQVVAIASNGGGKQALETVQRLLPVLCQA-HGLTPEQVVAIASNIGGKQALETVQALLPVLCQA-HGLTPEQVVAIASNIGGKQALETVQALLPVLCQA-HGLTPEQVVAIASHDGGKQALETVQRLLPVLCQA-HGLTPEQVVAIASHDGGKQALETVQRLLPVLCQA-HGLTPEQVVAIASHDGGKQALETVQRLLPVLCQA-HGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAAG-LTPEQVVAIASHDGGKQALETVQRLLPVL  861
                                   195|      206       216       226       236       246       256       266       276       286       296       306       316   |     -         -         -         -|      330       340       350   | | 359       369       379        |-|      398       408       418   | | 427       437       447        |-         -         -         -     | 461       471       481        |-         -         -         -     | 495       505       515        |-|      534       544       554   |     -         -         -         -|      568       578       588   | | 597       607       617        |-|      636       646       656   | | 665       675       685        |-|      704       714       724   | | 733       743       753        |-|      772       782       792   | | 801       811       821       831| |    840       850       860 
                                  193||                                                                                                                        320                                  321                              354 |                              388 |                              422 |                              456                                  457                              490                                  491                              524 |                              558                                  559                              592 |                              626 |                              660 |                              694 |                              728 |                              762 |                              796 |                                832 |                            
                                   195|                                                                                                                                                                                                355                                389                                423                                                                                                                                                                            525                                                                                                      593                                627                                661                                695                                729                                763                                797                                  833                            
                                    197                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:DNA  Length:22
                                                       
                2ypf B   -2 TTTATATAAACCTAACCCTCTA   19
                                     7        17  


Chain C from PDB  Type:DNA  Length:21
                                                      
                2ypf C  -19 TAGAGGGTTAGGTTTATATAA    1
                                   -10         0
   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 2YPF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YPF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YPF)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q3ZD73_XANCA | Q3ZD73)

Chain A   (AVRB3_XANEU | P14727)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0034053    modulation by symbiont of host defense-related programmed cell death    Any process in which an organism modulates the frequency, rate or extent of defense-related programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0052026    modulation by symbiont of host transcription    Any process in which an organism modulates the frequency, rate or extent of its host's transcription. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:201 - Ala A:202   [ RasMol ]  
    Ala A:216 - Leu A:217   [ RasMol ]  
    Ala A:220 - Thr A:221   [ RasMol ]  
    Arg A:236 - Ala A:237   [ RasMol ]  
    Leu A:287 - Asn A:288   [ RasMol ]  
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 Related Entries

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