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(-) Description

Title :  THE STRUCTURE OF TRWC COMPLEXED WITH A 27-MER DNA COMPRISING THE RECOGNITION HAIRPIN AND THE CLEAVAGE SITE
 
Authors :  R. Boer, S. Russi, A. Guasch, M. Lucas, A. G. Blanco, R. Perez-Luque, M. Coll, F. De La Cruz
Date :  25 Jan 06  (Deposition) - 31 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dna/Dna-Binding Protein, Relaxase, Bacterial Conjugation, Dna Transfer, Dna-Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Boer, S. Russi, A. Guasch, M. Lucas, A. G. Blanco, R. Perez-Luque, M. Coll, F. De La Cruz
Unveiling The Molecular Mechanism Of A Conjugative Relaxase: The Structure Of Trwc Complexed With A 27-Mer Dna Comprising The Recognition Hairpin And The Cleavage Site.
J. Mol. Biol. V. 358 857 2006
PubMed-ID: 16540117  |  Reference-DOI: 10.1016/J.JMB.2006.02.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRWC
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSU1621
    Expression System StrainC43(DE3)
    Expression System Taxid562
    Expression System VectorPET3A
    FragmentN-TERMINAL DOMAIN, RESIDUES 1-293
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsSELENO METHIONINE DERIVATIVE
    Other Details - SourceFROM THE PLASMID R388
 
Molecule 2 - 5'-D(*GP*CP*GP*CP*AP*CP*CP*GP*AP*AP *AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*GP*TP*CP*TP*AP*T)-3'
    ChainsB, D
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsFROM THE PLASMID R388
    SynonymORIT
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:150 , GLU A:151 , THR A:152 , ARG A:156 , HOH A:2120BINDING SITE FOR RESIDUE SO4 A1294
2AC2SOFTWAREHIS C:150 , GLU C:151 , THR C:152 , ARG C:156 , HOH C:2097BINDING SITE FOR RESIDUE SO4 C1294

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CDM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CDM)

(-) 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:280
 aligned with Q47673_ECOLX | Q47673 from UniProtKB/TrEMBL  Length:966

    Alignment length:293
                                    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       280       290   
         Q47673_ECOLX     1 MLSHMVLTRQDIGRAASYYEDGADDYYAKDGDASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRIMRSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETTGNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQLRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAEWQATAKELGIDFS 293
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhh.......-------------.eeeehhhhhhh......hhhhhhhhhh....................eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.....eeeeeeee.....eeeeeeeeee..ee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...eeee...hhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cdm A   1 mLSHmVLTRQDIGRAASFY-------------ASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRImRSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETTGNLVIGKFRHETSRERDPQLHTHAVILNmTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQLRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAEWQATAKELGIDFS 293
                            |   |   10        |-         -  |     40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   
                            |   |            19            33                                   70-MSE                                                                                            169-MSE                                                                                                                        
                            1-MSE                                                                                                                                                                                                                                                                                                
                                5-MSE                                                                                                                                                                                                                                                                                            

Chain B from PDB  Type:DNA  Length:25
                                                         
                 2cdm B   2 CGCACCGAAAGGTGCGTATTGTCTA  26
                                    11        21     

Chain C from PDB  Type:PROTEIN  Length:280
 aligned with Q47673_ECOLX | Q47673 from UniProtKB/TrEMBL  Length:966

    Alignment length:293
                                    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       280       290   
         Q47673_ECOLX     1 MLSHMVLTRQDIGRAASYYEDGADDYYAKDGDASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRIMRSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETTGNLVIGKFRHETSRERDPQLHTHAVILNMTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQLRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAEWQATAKELGIDFS 293
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhh.......-------------.eeeehhhhhh.......hhhhhhhhhhh...................eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.....eeeeeeee.....eeeeeeeeee..ee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eee...hhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cdm C   1 mLSHmVLTRQDIGRAASFY-------------ASEWQGKGAEELGLSGEVDSKRFRELLAGNIGEGHRImRSATRQDSKERIGLDLTFSAPKSVSLQALVAGDAEIIKAHDRAVARTLEQAEARAQARQKIQGKTRIETTGNLVIGKFRHETSRERDPQLHTHAVILNmTKRSDGQWRALKNDEIVKATRYLGAVYNAELAHELQKLGYQLRYGKDGNFDLAHIDRQQIEGFSKRTEQIAEWYAARGLDPNSVSLEQKQAAKVLSRAKKTSVDREALRAEWQATAKELGIDFS 293
                            |   |   10        |-         -  |     40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   
                            1-MSE            19            33                                   70-MSE                                                                                            169-MSE                                                                                                                        
                                5-MSE                                                                                                                                                                                                                                                                                            

Chain D from PDB  Type:DNA  Length:24
                                                        
                 2cdm D   2 CGCACCGAAAGGTGCGTATTGTCT  25
                                    11        21    

   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 2CDM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q47673_ECOLX | Q47673)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q47673_ECOLX | Q476731omh 1osb 1qx0 1s6m 1zm5 4pcb

(-) Related Entries Specified in the PDB File

1omh CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL-FREE STRUCTURE.
1osb CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL-FREE STRUCTURE.
1qx0 CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL-BOUND STRUCTURE