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(-) Description

Title :  CRYSTAL STRUCTURE OF THE F PLASMID TRAI RELAXASE DOMAIN WITH THE SCISSILE THYMIDINE BASE AND IMIDODIPHOSPHATE
 
Authors :  S. A. Lujan, M. R. Redinbo
Date :  07 Jun 07  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Relaxase, Hydrolase, Conjugation, Alternative Initiation, Atp-Binding, Dna-Binding, Helicase, Nucleotide-Binding, Plasmid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Lujan, L. M. Guogas, H. Ragonese, S. W. Matson, M. R. Redinbo
Disrupting Antibiotic Resistance Propagation By Inhibiting The Conjugative Dna Relaxase.
Proc. Natl. Acad. Sci. Usa V. 104 12282 2007
PubMed-ID: 17630285  |  Reference-DOI: 10.1073/PNAS.0702760104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN TRAI
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB2
    Expression System Strain: BL21 (DE3)
    Expression System Vector Type: PLASMID
    Fragment: RELAXASE DOMAIN (UNP RESIDUES 1-300)
    Gene: TRAI
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Strain: TRAI
    Synonym: DNA HELICASE I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PON1Ligand/IonIMIDO DIPHOSPHATE
3TMP1Ligand/IonTHYMIDINE-5'-PHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PON1Ligand/IonIMIDO DIPHOSPHATE
3TMP1Ligand/IonTHYMIDINE-5'-PHOSPHATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PON-1Ligand/IonIMIDO DIPHOSPHATE
3TMP-1Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:16 , HIS A:146 , HIS A:157 , HIS A:159BINDING SITE FOR RESIDUE MG A 3001
2AC2SOFTWAREASN A:22 , HIS A:146 , ASP A:147 , THR A:148 , SER A:149BINDING SITE FOR RESIDUE PON A 3002
3AC3SOFTWAREPHE A:16 , ARG A:68 , ARG A:150BINDING SITE FOR RESIDUE TMP A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q7U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q7U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q7U)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q7U)

(-) 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:268
 aligned with TRAI1_ECOLI | P14565 from UniProtKB/Swiss-Prot  Length:1756

    Alignment length:300
                                    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       300
         TRAI1_ECOLI      1 MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRAD  300
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh.......eeehhhhhh.......hhhhhhhhhhh..........ee..ee....eeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeee..--..eeee....eeeeeee..........eeeeeee..eee..eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhhh.ee....hhhhhh..------------------------------.hhhhhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2q7u A    1 MMSIAQVRSAGSAGNFYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMT--QSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGR------------------------------VDPEIKMAEWMQTLKETGFDIRAYRDAADQRAD  300
                                    10        20        30        40        50        60        70        80        90       100       110       120      |130       140       150       160       170       180       190       200       210       220       230      |  -         -         -       270       280       290       300
                                                                                                                                                        127  |                                                                                                        237                            268                                
                                                                                                                                                           130                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with TRAI1_ECOLI | P14565 from UniProtKB/Swiss-Prot  Length:1756

    Alignment length:300
                                    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       300
         TRAI1_ECOLI      1 MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRAD  300
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----TrwC-2q7uB01 B:1006-1288                                                                                                                                                                                                                                                                   ------------ Pfam domains (1)
           Pfam domains (2) -----TrwC-2q7uB02 B:1006-1288                                                                                                                                                                                                                                                                   ------------ Pfam domains (2)
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh........eeehhhhhh.......hhhhhhhhhh.......--------......eeeeeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...ee..hhhhh...ee.....eeeeeeee.....eeeeeeeeee....................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee......ee.....hhhhh----------------------------..-..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2q7u B 1001 MMSIAQVRSAGSAGNFYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGA--------SNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFS----------------------------SK-HVDPEIKMAEWMQTLKETGFDIRAYRDAADQRAD 1300
                                  1010      1020      1030      1040      1050      1060   |     -  |   1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230    |    -         -         -   || 1270      1280      1290      1300
                                                                                        1064     1073                                                                                                                                                              1235                         1264| |                                 
                                                                                                                                                                                                                                                                                                 1265 |                                 
                                                                                                                                                                                                                                                                                                   1267
   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 2Q7U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q7U)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: TrwC] (9)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRAI1_ECOLI | P14565)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0003917    DNA topoisomerase type I activity    Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  TRAI1_ECOLI | P14565
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  3.6.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRAI1_ECOLI | P14565: 1p4d 2a0i 2l8b 2q7t 3fld

(-) Related Entries Specified in the PDB File

1a0i F PLASMID TRAI WITH UNCLEAVED ORIT DNA
1omh METAL FREE R388 TRWC WITH ORIT DNA
1osb METAL FREE R388 TRWC WITH ORIT DNA
1p4d APO F PLASMID TRAI
1qx0 R388 TRWC WITH ORIT DNA
2cdm R388 TRWC WITH ORIT DNA
2q7t