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(-) Description

Title :  CRYSTAL STRUCTURE OF AGROBACTERIUM TUMEFACIENS VIRE2 IN COMPLEX WITH ITS CHAPERONE VIRE1: A NOVEL FOLD AND IMPLICATIONS FOR DNA BINDING
 
Authors :  O. Dym, S. Albeck, T. Unger, M. Elbaum, Israel Structural Proteomics (Ispc)
Date :  30 Dec 07  (Deposition) - 19 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Unique Topology, Novel Fold, Structural Genomics, Israel Structural Proteomics Center, Ispc, Crown Gall Tumor, Dna-Binding, Secreted, Virulence, Dna Binding Protein, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Dym, S. Albeck, T. Unger, J. Jacobovitch, A. Branzburg, Y. Michael, D. Frenkiel-Krispin, S. G. Wolf, M. Elbaum
Crystal Structure Of The Agrobacterium Virulence Complex Vire1-Vire2 Reveals A Flexible Protein That Can Accommodate Different Partners.
Proc. Natl. Acad. Sci. Usa V. 105 11170 2008
PubMed-ID: 18678909  |  Reference-DOI: 10.1073/PNAS.0801525105

(-) Compounds

Molecule 1 - SINGLE-STRAND DNA-BINDING PROTEIN
    Atcc: 33970
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYCDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: VIRE2, ATU6190, AGR_PTI_28
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Strain: C58
    Synonym: 63.5 KDA VIRULENCE PROTEIN
 
Molecule 2 - PROTEIN VIRE1
    Atcc: 33970
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYCDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: VIRE1, ATU6189, AGR_PTI_26
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Strain: C58
    Synonym: 7.1 KDA VIRULENCE PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NH43Ligand/IonAMMONIUM ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:248 , TYR A:250BINDING SITE FOR RESIDUE NH4 A 601
2AC2SOFTWAREHIS B:31 , GLN B:32 , SER B:33 , GLY B:35BINDING SITE FOR RESIDUE NH4 B 603
3AC3SOFTWAREASP A:154 , GLY A:155 , ARG A:168 , GLU B:47BINDING SITE FOR RESIDUE PEG A 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BTP)

(-) 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:386
 aligned with VIRE2_AGRFC | P08062 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:406
                                   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       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511      
          VIRE2_AGRFC   112 RRTDEYILVRQTGQDKFAGTTKCNLDHLPTKAEFNASCRLYRDGVGNYYPPPLAFERIDIPEQLAAQLHNLEPREQSKQCFQYKLEVWNRAHAEMGITGTDIFYQTDKNIKLDRNYKLRPEDRYIQTEKYGRREIQKRYEHQFQAGSLLPDILIKTPQNDIHFSYRFAGDAYANKRFEEFERAIKTKYGSDTEIKLKSKSGIMHDSKYLESWERGSADIRFAEFAGENRAHNKQFPAATVNMGRQPDGQGGMTRDRHVSVDYLLQNLPNSPWTQALKEGKLWDRVQVLARDGNRYMSPSRLEYSDPEHFTQLMDQVGLPVSMGRQSHANSVKFEQFDRQAAVIVADGPNLREVPDLSPEKLQQLSQKDVLIADRNEKGQRTGTYTNVVEYERLMMKLPSDAAQLLA 517
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee..eeeeee.hhh....hhhhhhhheeeee.....eehhhhhhhh...hhhhhhh.--...hhhhhhhhhhhhhhhhhhhhhhh......................hhhh.eee.....eee.................eeee.....eeee...........hhhhhhhhhhhhhh...eeeee.....eeehhhhhhhh.hhhhhhhhhhh.....---....eeee.....-----....eeeehhhhhhhh..hhhhhhhhh..hhh.eeee.....eeehhhhhhhhhhhhhhhhhhhhh.hhhhhhh...-------......eeee...eee.hhhh.....---....eeeeee.....eeeeeeehhhhhhh....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3btp A 112 RRTDEYILVRQTGQDKFAGTTKCNLDHLPTKAEFNASCRLYRDGVGNYYPPPLAFERIDLPEQLAAQL--LEPREQSKQCFQYKLEVWNRAHAEMGITGTDIFYQTDKNIKLDRNYKLRPEDRYIQTEKYGRREIQKRYEHQFQAGSLLPDILIKTPQNDIHFSYRFAGDAYANKRFEEFERAIKTKYGSDTEIKLKSKSGIMHDSKYLESWERGSADIRFAEFAGENRA---QFPAATVNMGRQP-----MTRDRHVSVDYLLQNLPNSPWTQALKEGKLWDRVQVLARDGNRYMSPSRLEYSDPEHFTQLMDQVGLPVSMGRQSHA-------FDRQAAVIVADGPNLREVPDLSPEKL---SQKDVLIADRNEKGQRTGTYTNVVEYERLMMKLPSDAAQLLA 517
                                   121       131       141       151       161       171       | -|      191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   |   351     |   - |     371       381       391       401       411       421       431       | -     | 451       461       471|   |  481       491       501       511      
                                                                                             179  |                                                                                                                                                            341 345         357   363                                                                         439     447                      472 476                                         
                                                                                                182                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:28
 aligned with VIRE1_AGRFC | P08063 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:28
                                    40        50        
          VIRE1_AGRFC    31 HHQSNGFTSLDLEMIELENFVLHCPLPE  58
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 3btp B  30 HHQSNGFTSLDLEMIELENFVLHCPLPE  57
                                    39        49
   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 3BTP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VIRE2_AGRFC | P08062)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic 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).
biological process
    GO:0009294    DNA mediated transformation    The introduction and uptake of foreign genetic material (DNA or RNA) into a cell, and often the expression of that genetic material.
    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.
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.

Chain B   (VIRE1_AGRFC | P08063)
molecular function
    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).
biological process
    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:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.

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 Related Entries

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        VIRE2_AGRFC | P08062: 4blf

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