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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF AGROBACTERIUM RADIOBACTER K84 AGNB2 LEURS-TRNA-LEUAMS
 
Authors :  A. Palencia, S. Chopra, C. Virus, S. Schulwitz, B. R. Temple, S. Cusack, J. S. Reader
Date :  05 Feb 15  (Deposition) - 17 Feb 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Ligase-Rna Complex, Leucine-Trna, Leucine-Trna Ligase Activity Atp + L-Leucine + Trna(Leu) Gives Amp + Diphosphate + L-Leucyl-Trna(Leu), Aminoacyl- Trna Editing Activity, Aminoacyl-Trna Synthetase, Protein Biosynthesis, Toxic Moeity 84 Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chopra, A. Palencia, C. Virus, S. Schulwitz, B. R. Temple, S. Cusack J. Reader
Structural Characterization Of Antibiotic Self-Immunity Trna Synthetase In Plant Tumour Biocontrol Agent.
Nat. Commun. V. 7 12928 2016
PubMed-ID: 27713402  |  Reference-DOI: 10.1038/NCOMMS12928

(-) Compounds

Molecule 1 - LEUCINE--TRNA LIGASE
    Atcc: BAA-868
    Chains: A, B
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: AGROBACTERIUM RADIOBACTER K84
    Organism Taxid: 311403
    Synonym: LEUCYL-TRNA SYNTHETASE
 
Molecule 2 - TRNA-LEU TAA ISOACCEPTOR
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358
    Strain: C58

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B D
Biological Unit 2 (1x): A C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1LSS2Ligand/Ion5'-O-(L-LEUCYLSULFAMOYL)ADENOSINE
2MN2Ligand/IonMANGANESE (II) ION
3SO45Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1LSS1Ligand/Ion5'-O-(L-LEUCYLSULFAMOYL)ADENOSINE
2MN-1Ligand/IonMANGANESE (II) ION
3SO43Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1LSS1Ligand/Ion5'-O-(L-LEUCYLSULFAMOYL)ADENOSINE
2MN-1Ligand/IonMANGANESE (II) ION
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:432 , CYS A:435 , CYS A:473 , CYS A:476BINDING SITE FOR RESIDUE ZN A 900
02AC2SOFTWARECYS B:432 , CYS B:435 , CYS B:473 , CYS B:476BINDING SITE FOR RESIDUE ZN B 900
03AC3SOFTWAREMET A:38 , PHE A:39 , PRO A:40 , TYR A:41 , HIS A:47 , GLY A:49 , HIS A:50 , ASN A:53 , TYR A:54 , ASP A:78 , SER A:493 , TYR A:496 , TYR A:523 , GLY A:525 , GLY A:526 , GLU A:528 , HIS A:529 , HIS A:533 , GLN A:562 , GLY A:563 , MET A:564 , VAL A:565 , HOH A:2034 , HOH A:2231BINDING SITE FOR RESIDUE LSS A1818
04AC4SOFTWAREMET B:38 , PHE B:39 , PRO B:40 , TYR B:41 , HIS B:47 , GLY B:49 , HIS B:50 , ASN B:53 , TYR B:54 , ASP B:78 , SER B:493 , TYR B:496 , TYR B:523 , GLY B:525 , GLY B:526 , GLU B:528 , HIS B:529 , HIS B:533 , GLN B:562 , GLY B:563 , MET B:564 , VAL B:565 , HOH B:2064 , HOH B:2266 , HOH B:2384BINDING SITE FOR RESIDUE LSS B1818
05AC5SOFTWAREG C:1BINDING SITE FOR RESIDUE MN C1077
06AC6SOFTWAREG D:1BINDING SITE FOR RESIDUE MN D1077
07AC7SOFTWARESER A:213 , G C:5 , G C:69 , G C:70 , HOH C:2086 , HOH C:2089BINDING SITE FOR RESIDUE SO4 C1078
08AC8SOFTWARESER B:213 , G D:5 , G D:69 , G D:70 , HOH D:2074BINDING SITE FOR RESIDUE SO4 D1078
09AC9SOFTWAREARG A:766 , THR A:767 , MET A:768 , THR A:769 , HOH A:2302BINDING SITE FOR RESIDUE SO4 A1819
10BC1SOFTWARELYS B:31 , ARG B:67 , TYR B:69BINDING SITE FOR RESIDUE SO4 B1819
11BC2SOFTWAREARG B:766 , THR B:767 , MET B:768 , THR B:769 , HOH B:2366BINDING SITE FOR RESIDUE SO4 B1820

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AH5)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:445 -Pro A:446
2Ala A:518 -Pro A:519
3Leu B:445 -Pro B:446
4Ala B:518 -Pro B:519

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AH5)

(-) Exons   (0, 0)

(no "Exon" information available for 5AH5)

(-) 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:789
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...........eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.ee..ee.......eeeeeeeeee.hhhhhhhhhhh.......hhhhhhhhhhhhheeeeeee..ee........eee.hhhhhhhh........hhhhhh..hhhhhhhhhhhh.hhhhhhh....eeeeeeeeee....eeeeeeee.................hhhhhhhhhhh..............hhhhhhhhhhhhhhhhh..eeeeee....ee.ee.....ee..eeee...eeee.hhhhh...............hhhhhhhhheee......eeee...eehhhhhhhhhhhh..........hhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh........eeeee....ee...............hhhhhhhhhhhhhhhhhhhhh......ee.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhh.............eeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhh...eeeeeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ah5 A   2 QYDHRSRDAFWQQKWDEKRIFDWDPSSPGKKFYVLEMFPYTSGHLHIGHVRNYSMGDTLARMQIARGYSVLHPMGWDSFGLPAENAARKFGTHPAKFTQDAIDSMKRSMMQLGFGYSWANELATCSPTYVLAQQKLFLDLYRKGLIYRDDTYVYWDPVEQTVLAAEQVIDGKGWRSGAAVYKRRTPQWFVDIRSYADRLLDDLESLEGWPTSVRNIQRNWIGRTEGAEVRFLVEASDLTINAFTTRLDTLAGCTFIALAPEHTILDEMRASVKDYCESILVLSSEERSAGAKSGIFTGLMVVNPLNQERVPLYVANYVMPDFGTGAVIGVPDERDADFGALFGLPVRVVSHSLVDGLTSSAAREILIAHLSEKLEGQKSTQYRLQNWSISRQRYWGCPIPIIHCSECGTIPVAEEQLPILLPDHLISEGSGSPLSRDESWMKAKCPQCGGDAARDPDTMDTFVDSSWYFLRYPSPSSPNPIDSSLCNKIAPADVYIGGIEHATLHLIYSRFITKVLHDLGYIEFDEPFVELYNQGMVNDVHGRKQSKSLGNVTDPSVVVQEFGADAVRCYLLFKTTYNAPINWEDSGPQAMRSYLERVCRLFTNNLDRLRSSSAIEICPDDCENEEDREIARQLQLAIGKVTADVERFHFNAAIAAIMSVTNLLYEKGGKASPTVLAGSLRLLVRLLAPFAPHISEELWALSGCNSLVAAEPWPTINERLVQAENIVLPVQINGKLIRTMTIPVNLAEEDILSTVLALPEVRSRLSDRDLKNYRYVPNRIINLVVGLEH 817
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261      |277       287       297       307       317       327       337||     349       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808         
                                                                                                                                                                                                                                                                                                    268|                                                            338|              358|                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                     275                                                             341               378                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:771
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...........eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.ee..ee.......eeeeeeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhheeeeeee..ee........eee.hhhhh.....eee........hhhhhhhhhhhhh............eeeeeeeeee....eeeeeeee..........ee....hhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeee....ee.ee.....ee..eeee...eeee.hhhhh...............hhhhhhhhheee......eeee...eehhhhhhhhhhhh..........hhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh........eeeee....ee.......hhhhh...hhhhhhhhhhhhhhhhhhhhh......ee.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhh.............eeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ah5 B   2 QYDHRSRDAFWQQKWDEKRIFDWDPSSPGKKFYVLEMFPYTSGHLHIGHVRNYSMGDTLARMQIARGYSVLHPMGWDSFGLPAENAARKFGTHPAKFTQDAIDSMKRSMMQLGFGYSWANELATCSPTYVLAQQKLFLDLYRKGLIYRDDTYVYWDPVEQTVLAAEQVIDGKGWRSGAAVYKRRTPQWFVDIRSYADRLLDDLESLEGWPTSVRNIQRNWIGRTEGAEVRFLVEASDLTINAFTTRLDTLAGCTFIALAPEHTILDRASVKDYCESILVLSSEERSAGAKSGIFTGLMVVNPLNQERVPLYVANYVMPDFGTGAVIGVPDERDADFGALTSSAAREILIAHLSEKLEGQKSTQYRLQNWSISRQRYWGCPIPIIHCSECGTIPVAEEQLPILLPDHLISEGSGSPLSRDESWMKAKCPQCGGDAARDPDTMDTFVDSSWYFLRYPSPSSPNPIDSSLCNKIAPADVYIGGIEHATLHLIYSRFITKVLHDLGYIEFDEPFVELYNQGMVNDVHGRKQSKSLGNVTDPSVVVQEFGADAVRCYLLFKTTYNAPINWEDSGPQAMRSYLERVCRLFTNNLDRLRSSSAIEICPDDCENEEDREIARQLQLAIGKVTADVERFHFNAAIAAIMSVTNLLYEKGGKASPTVLAGSLRLLVRLLAPFAPHISEELWALSGCNSLVAAEPWPTINERLVQAENIVLPVQINGKLIRTMTIPVNLAEEDILSTVLALPEVRSRLSDRDLKNYRYVPNRIINLVVGLEH 817
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     ||279       289       299       309       319       329       341       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816 
                                                                                                                                                                                                                                                                                                   267|                                                           338|      350|                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                    276                                                            341       386                                                                                                                                                                                                                                                                                                                                                                                                                                               


Chain C from PDB  Type:RNA  Length:80
                                                                                                                
                 5ah5 C   1 GCCCGCAUGGUGAAAUCGGUAAACACAUCGCACAAUGCGCCGCCUCUGGCUUGCCGGUUCAAGUCCGGCUGCGGGCACCA  76
                                    10        20|       29  ||    43   ||||46G        56        66        76
                                              20A          32|       46A||||||                              
                                                            37        46B|||||                              
                                                                       46C||||                              
                                                                        46D|||                              
                                                                         46E||                              
                                                                          46F|                              
                                                                           46G                              


Chain D from PDB  Type:RNA  Length:81
                                                                                                                 
                 5ah5 D   1 GCCCGCAUGGUGAAAUCGGUAAACACAUCGCACUAAUGCGCCGCCUCUGGCUUGCCGGUUCAAGUCCGGCUGCGGGCACCA  76
                                    10        20|       29   ||   42    |||46F|       55        65        75 
                                              20A           33|       46A||||||                              
                                                             37        46B|||||                              
                                                                        46C||||                              
                                                                         46D|||                              
                                                                          46E||                              
                                                                           46F|                              
                                                                            46G
   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 5AH5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AH5)

(-) Gene Ontology  (11, 11)

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 Related Entries

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(-) Related Entries Specified in the PDB File

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