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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PLASMID PCU1 TRAI RELAXASE DOMAIN
 
Authors :  M. R. Redinbo, R. P. Nash
Date :  21 Dec 09  (Deposition) - 19 May 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
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: PTYB2
    Expression System Strain: BL21(DE3)
    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  (4, 30)

Asymmetric Unit (4, 30)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO26Ligand/Ion1,2-ETHANEDIOL
3MN32Ligand/IonMANGANESE (III) ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 22)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO19Ligand/Ion1,2-ETHANEDIOL
3MN31Ligand/IonMANGANESE (III) ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CIT-1Ligand/IonCITRIC ACID
2EDO7Ligand/Ion1,2-ETHANEDIOL
3MN31Ligand/IonMANGANESE (III) ION
4PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:149 , HIS A:160 , HIS A:162 , CIT A:321BINDING SITE FOR RESIDUE MN3 A 300
02AC2SOFTWAREARG A:9 , GLN A:10 , ASN A:11 , VAL A:12 , THR A:13BINDING SITE FOR RESIDUE EDO A 301
03AC3SOFTWARESER A:35 , TRP A:36 , SER A:47 , GLY A:48 , HOH A:341BINDING SITE FOR RESIDUE EDO A 302
04AC4SOFTWARESER A:28 , PHE A:33 , THR A:34 , ARG A:148BINDING SITE FOR RESIDUE EDO A 303
05AC5SOFTWAREASP A:24 , SER A:52 , EDO A:310 , HOH A:323 , HOH A:428BINDING SITE FOR RESIDUE EDO A 304
06AC6SOFTWARETHR A:104 , GLU A:107 , ALA A:108 , LYS A:111 , GLU A:202BINDING SITE FOR RESIDUE EDO A 305
07AC7SOFTWAREHOH A:462 , THR B:104 , GLU B:107BINDING SITE FOR RESIDUE EDO A 306
08AC8SOFTWAREGLN A:125 , LYS A:180 , ASP A:182 , GLU A:183 , ARG A:186BINDING SITE FOR RESIDUE EDO A 307
09AC9SOFTWAREALA A:115 , ARG A:118BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWARESER A:20 , SER A:52 , ALA A:53 , LYS A:56 , EDO A:304BINDING SITE FOR RESIDUE EDO A 310
11BC2SOFTWARELEU A:210 , TYR A:212 , EDO A:317BINDING SITE FOR RESIDUE EDO A 311
12BC3SOFTWAREVAL A:60 , HOH A:464BINDING SITE FOR RESIDUE EDO A 312
13BC4SOFTWAREARG A:54 , GLU A:57 , ILE A:63 , ASP A:64 , HOH A:326BINDING SITE FOR RESIDUE EDO A 313
14BC5SOFTWAREHOH A:454 , HOH B:352BINDING SITE FOR RESIDUE EDO A 315
15BC6SOFTWAREARG A:186 , ASN A:187 , LYS A:188 , MET A:189 , HIS A:190 , HOH A:368 , HOH A:374 , GLN B:197 , LEU B:201BINDING SITE FOR RESIDUE EDO A 316
16BC7SOFTWARETHR A:204 , TYR A:208 , GLU A:209 , LEU A:210 , TYR A:212 , EDO A:311BINDING SITE FOR RESIDUE EDO A 317
17BC8SOFTWARETYR A:212 , ASN A:213 , ASN A:217 , THR A:218 , LYS B:188 , MET B:189BINDING SITE FOR RESIDUE EDO A 318
18BC9SOFTWAREHIS A:149 , GLU A:150 , THR A:151 , GLN B:131BINDING SITE FOR RESIDUE EDO A 319
19CC1SOFTWAREARG A:171 , ARG A:177BINDING SITE FOR RESIDUE PO4 A 320
20CC2SOFTWAREHIS A:149 , HIS A:160 , HIS A:162 , MN3 A:300 , HOH A:357 , HOH A:392 , HOH A:410 , THR B:129 , GLN B:131 , GLY B:132BINDING SITE FOR RESIDUE CIT A 321
21CC3SOFTWAREHIS B:149 , HIS B:160 , HIS B:162 , HOH B:355BINDING SITE FOR RESIDUE MN3 B 300
22CC4SOFTWAREARG B:118BINDING SITE FOR RESIDUE EDO B 301
23CC5SOFTWARETYR A:212 , MET B:185 , ARG B:186 , ASN B:187 , LYS B:188 , MET B:189 , EDO B:304BINDING SITE FOR RESIDUE EDO B 302
24CC6SOFTWAREHOH A:462 , HOH A:474 , LYS B:103 , ILE B:106 , GLU B:107 , ARG B:148BINDING SITE FOR RESIDUE EDO B 303
25CC7SOFTWAREGLN A:197 , ALA A:200 , LEU A:201 , ARG B:186 , ASN B:187 , MET B:189 , HIS B:190 , EDO B:302 , HOH B:328 , HOH B:358BINDING SITE FOR RESIDUE EDO B 304
26CC8SOFTWARELYS A:215 , MET B:1 , SER B:88 , ALA B:89 , PRO B:90 , HOH B:365BINDING SITE FOR RESIDUE EDO B 305
27CC9SOFTWARETHR B:128 , GLN B:137 , ARG B:171 , GLU B:172 , ASP B:173BINDING SITE FOR RESIDUE EDO B 306
28DC1SOFTWAREVAL B:15 , VAL B:16 , PHE B:147 , HIS B:149 , PHE B:164BINDING SITE FOR RESIDUE EDO B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L57)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L57)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L57)

(-) Exons   (0, 0)

(no "Exon" information available for 3L57)

(-) 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:223
 aligned with Q9X4G2_ECOLX | Q9X4G2 from UniProtKB/TrEMBL  Length:1078

    Alignment length:225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
         Q9X4G2_ECOLX     1 MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQRHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTNNLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYELRYNSKNNTFDMAHFS 225
               SCOP domains d3l57a_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhh..................eeeehhhhhhh......hhhhhhhhhh.eee..ee......hhhh.eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeee....eeeee.....eeeeeeee..--..eeeeeeeee..ee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l57 A   1 MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQRHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTNNLVVATFRHETSR--DPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYELRYNSKNNTFDMAHFS 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  |  | 160       170       180       190       200       210       220     
                                                                                                                                                                                  153  |                                                                     
                                                                                                                                                                                     156                                                                     


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

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         Q9X4G2_ECOLX     1 MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQRHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTNNLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYELRYNSKNNTFDMAH 223
               SCOP domains d3l57b_ B: automa               ted matches                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------TrwC-3l57B               01 B:8-223                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) -------TrwC-3l57B               02 B:8-223                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author .eeeeeee.........---------------.eeeehhhhhhh......hhhhhhhhhhh...........----...eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee.....eeeeee....-.....eeeeeee..ee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l57 B   1 MLDITTITRQNVTSVVG---------------FTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQRH----KKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTNNLVVATFRHETSR-LDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYELRYNSKNNTFDMAH 223
                                    10      |  -         -  |     40        50        60        70 |    | 80        90       100       110       120       130       140       150  | |  160       170       180       190       200       210       220   
                                           17              33                                     72   77                                                                         153 |                                                                    
                                                                                                                                                                                    155
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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 3L57)

(-) 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 3L57)

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  3l57
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 Related Entries

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        Q9X4G2_ECOLX | Q9X4G2: 3l6t

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