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(-) Description

Title :  CRYSTAL STRUCTURE OF AN N-TERMINAL MUTANT OF THE PLASMID PCU1 TRAI RELAXASE DOMAIN
 
Authors :  M. R. Redinbo, R. P. Nash
Date :  24 Dec 09  (Deposition) - 19 May 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Trwc Superfamily Of Relaxase Enzymes, Conjugative Relaxase, Mob Class Relaxase, Conjugal Nickase, Hydrolase, Histidine Triad, Huh+H Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Nash, S. Habibi, Y. Cheng, S. A. Lujan, M. R. Redinbo
The Mechanism And Control Of Dna Transfer By The Conjugativ Relaxase Of Resistance Plasmid Pcu1.
Nucleic Acids Res. V. 38 5929 2010
PubMed-ID: 20448025  |  Reference-DOI: 10.1093/NAR/GKQ303

(-) Compounds

Molecule 1 - MOBILIZATION PROTEIN TRAI
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCGS9
    Expression System Strain: BL21AI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RELAXASE DOMAIN
    Gene: PMUR050_047, TRAI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: TRAI

 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  (7, 31)

Asymmetric Unit (7, 31)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL3Ligand/IonCHLORIDE ION
3EDO21Ligand/Ion1,2-ETHANEDIOL
4MG1Ligand/IonMAGNESIUM ION
5NA1Ligand/IonSODIUM ION
6NI2Ligand/IonNICKEL (II) ION
7PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO13Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NI-1Ligand/IonNICKEL (II) ION
7PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1CIT-1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO8Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NI-1Ligand/IonNICKEL (II) ION
7PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:-2 , VAL A:16 , HIS A:149 , HIS A:160 , HIS A:162 , EDO A:301 , EDO A:306 , NI A:314 , HOH A:360 , HOH A:381 , HOH A:463 , THR B:129 , GLN B:131 , GLY B:132BINDING SITE FOR RESIDUE CIT A 300
02AC2SOFTWAREASP A:84 , THR A:86 , HIS A:162 , CIT A:300 , HOH A:386 , HOH A:460 , HOH A:537BINDING SITE FOR RESIDUE EDO A 301
03AC3SOFTWAREARG A:186 , ASN A:187 , LYS A:188 , MET A:189 , HIS A:190 , HOH A:376 , HOH A:539 , LEU B:201 , EDO B:305 , HOH B:331BINDING SITE FOR RESIDUE EDO A 302
04AC4SOFTWARESER A:31 , SER A:32 , THR A:34 , SER A:35 , GLY A:48 , ASP A:49BINDING SITE FOR RESIDUE EDO A 303
05AC5SOFTWAREMET A:69 , GLN A:70 , ARG A:177 , ALA A:178 , HOH A:517BINDING SITE FOR RESIDUE EDO A 304
06AC6SOFTWARETHR A:104 , GLU A:107 , ALA A:108 , LYS A:111 , GLU A:202 , HOH A:406 , HOH A:476BINDING SITE FOR RESIDUE EDO A 305
07AC7SOFTWAREVAL A:16 , CIT A:300 , EDO A:308 , ARG B:130 , GLN B:131BINDING SITE FOR RESIDUE EDO A 306
08AC8SOFTWAREGLY A:38 , THR A:39 , ARG A:118 , GLU A:121 , HOH A:403 , HOH A:419 , HOH A:526BINDING SITE FOR RESIDUE EDO A 307
09AC9SOFTWAREVAL A:16 , GLY A:17 , TYR A:27 , HIS A:149 , EDO A:306 , HOH A:411 , HOH A:520 , GLN B:131BINDING SITE FOR RESIDUE EDO A 308
10BC1SOFTWARELYS A:56 , HOH A:359 , HOH A:369BINDING SITE FOR RESIDUE EDO A 309
11BC2SOFTWAREARG A:80 , ARG A:127 , ASN A:181 , ASP A:182 , CL A:315 , HOH A:333 , HOH A:334BINDING SITE FOR RESIDUE EDO A 310
12BC3SOFTWARETHR A:65 , HOH A:503BINDING SITE FOR RESIDUE EDO A 311
13BC4SOFTWAREARG A:9 , TYR A:18 , VAL A:60 , HOH A:427BINDING SITE FOR RESIDUE EDO A 312
14BC5SOFTWARETYR A:212 , ASN A:213 , SER A:214 , ASN A:217 , THR A:218 , LYS B:188BINDING SITE FOR RESIDUE EDO A 313
15BC6SOFTWAREHIS A:149 , HIS A:160 , HIS A:162 , CIT A:300BINDING SITE FOR RESIDUE NI A 314
16BC7SOFTWARELEU A:179 , ASN A:181 , EDO A:310BINDING SITE FOR RESIDUE CL A 315
17BC8SOFTWARELYS A:111 , ARG A:118BINDING SITE FOR RESIDUE CL A 316
18BC9SOFTWAREVAL A:16BINDING SITE FOR RESIDUE CL A 317
19CC1SOFTWAREARG A:171 , ARG A:177 , HOH A:332BINDING SITE FOR RESIDUE PO4 A 318
20CC2SOFTWAREMET A:1 , PRO A:90 , THR A:218 , PHE A:219 , NA A:321 , HOH A:375 , HOH A:429 , LYS B:215 , ASN B:216BINDING SITE FOR RESIDUE PO4 A 319
21CC3SOFTWARESER A:32 , PHE A:33 , GLU A:110 , THR A:146 , ARG A:148 , HOH A:396BINDING SITE FOR RESIDUE MG A 320
22CC4SOFTWARELYS A:91 , PO4 A:319BINDING SITE FOR RESIDUE NA A 321
23CC5SOFTWAREHOH A:495 , ARG B:186 , ASN B:187 , LYS B:188 , MET B:189 , HIS B:190 , EDO B:301 , HOH B:396BINDING SITE FOR RESIDUE EDO B 300
24CC6SOFTWAREMET B:185 , ARG B:186 , LYS B:188 , MET B:189 , EDO B:300BINDING SITE FOR RESIDUE EDO B 301
25CC7SOFTWAREHIS B:160 , HIS B:162 , NI B:308 , HOH B:323 , HOH B:435BINDING SITE FOR RESIDUE EDO B 302
26CC8SOFTWAREALA B:126 , ARG B:127 , ALA B:178BINDING SITE FOR RESIDUE EDO B 303
27CC9SOFTWARETHR B:67 , GLY B:174 , GLN B:175 , TRP B:176BINDING SITE FOR RESIDUE EDO B 304
28DC1SOFTWAREEDO A:302 , HOH A:345 , VAL B:194 , GLN B:197 , GLU B:198 , HOH B:367BINDING SITE FOR RESIDUE EDO B 305
29DC2SOFTWARELYS A:215 , HOH A:351 , PHE B:219 , HOH B:314 , HOH B:342 , HOH B:345 , HOH B:347 , HOH B:348BINDING SITE FOR RESIDUE EDO B 306
30DC3SOFTWAREVAL B:15 , ASP B:84 , PHE B:147 , PHE B:164BINDING SITE FOR RESIDUE EDO B 307
31DC4SOFTWAREHIS B:149 , HIS B:160 , HIS B:162 , EDO B:302 , HOH B:323BINDING SITE FOR RESIDUE NI B 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L6T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L6T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L6T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L6T)

(-) Exons   (0, 0)

(no "Exon" information available for 3L6T)

(-) 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:226
 aligned with Q9X4G2_ECOLX | Q9X4G2 from UniProtKB/TrEMBL  Length:1078

    Alignment length:228
                               1                                                                                                                                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217        
         Q9X4G2_ECOLX     - ---MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQRHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTNNLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYELRYNSKNNTFDMAHFS 225
               SCOP domains d3l6ta_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhh..................eeeehhhhhhh......hhhhhhhhhh.eee..ee......hhhh.eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee..--..eeee.....eeeeeeee......eeeeeeeee..ee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l6t A  -2 SNAMLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQRHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTR--KSVTQNTNNLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYELRYNSKNNTFDMAHFS 225
                                     7        17        27        37        47        57        67        77        87        97       107       117       127  |  | 137       147       157       167       177       187       197       207       217        
                                                                                                                                                              130  |                                                                                            
                                                                                                                                                                 133                                                                                            


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with Q9X4G2_ECOLX | Q9X4G2 from UniProtKB/TrEMBL  Length:1078

    Alignment length:226
                               1                                                                                                                                                                                                                              
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217      
         Q9X4G2_ECOLX     - ---MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQRHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTNNLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYELRYNSKNNTFDMAH 223
               SCOP domains d3l6tb_ B: automate                d matches                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------TrwC-3l6t                B01 B:8-223                                                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) ----------TrwC-3l6t                B02 B:8-223                                                                                                                                                                                     Pfam domains (2)
         Sec.struct. author ....eeeeeeehhhhh...----------------.eeeehhhhhhh......hhhhhhhhhh.eee..ee....----...eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee.....eeeeee..---.....eeeeeee..ee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6t B  -2 SNAMLDITTITRQNVTSVV----------------FTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQRH----KKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTNNLVVATFRHET---LDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYELRYNSKNNTFDMAH 223
                                     7        |-         -     |  37        47        57        67    |   77        87        97       107       117       127       137       147   |   157       167       177       187       197       207       217      
                                             16               33                                     72   77                                                                       151 155
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L6T)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3L6T)

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        Q9X4G2_ECOLX | Q9X4G2: 3l57

(-) Related Entries Specified in the PDB File

3l57 THE CRYSTAL STRUCTURE OF THE WILD TYPE PLASMID PCU1 TRAI RELAXASE DOMAIN