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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF GLYCYL TRNA SYNTHETASE (GLYRS) FROM AQUIFEX AEOLICUS IN COMPLEX WITH AN ANALOG OF GLYCYL ADENYLATE (GLY-SA)
 
Authors :  M. I. Valencia-Sanchez, A. Torres-Larios
Date :  04 Dec 15  (Deposition) - 11 May 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,E  (1x)
Keywords :  Class Ii Trna Synthetase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. I. Valencia-Sanchez, A. Rodriguez-Hernandez, R. Ferreira, H. A. Santamaria-Suarez, M. Arciniega, A. C. Dock-Bregeon, D. Moras, B. Beinsteiner, H. Mertens, D. Svergun, L. G. Brieba, M. Grtli, A. Torres-Larios
Structural Insights Into The Polyphyletic Origins Of Glycyl Trna Synthetases.
J. Biol. Chem. V. 291 14430 2016
PubMed-ID: 27226617  |  Reference-DOI: 10.1074/JBC.M116.730382

(-) Compounds

Molecule 1 - GLYCINE--TRNA LIGASE ALPHA SUBUNIT
    Chains: A, B, C, D, E
    EC Number: 6.1.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GLYQ, AQ_945
    Organism Scientific: AQUIFEX AEOLICUS (STRAIN VF5)
    Organism Taxid: 224324
    Strain: VF5
    Synonym: GLYCYL-TRNA SYNTHETASE ALPHA SUBUNIT,GLYRS

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): A    
Biological Unit 2 (1x):  BC  
Biological Unit 3 (1x):    DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1G5A5Ligand/Ion5'-O-(GLYCYLSULFAMOYL)ADENOSINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1G5A2Ligand/Ion5'-O-(GLYCYLSULFAMOYL)ADENOSINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1G5A2Ligand/Ion5'-O-(GLYCYLSULFAMOYL)ADENOSINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1G5A2Ligand/Ion5'-O-(GLYCYLSULFAMOYL)ADENOSINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:33 , ARG A:58 , ASP A:61 , ASN A:69 , ARG A:70 , LEU A:71 , TYR A:74 , GLN A:76 , TRP A:115 , GLU A:135 , ILE A:136 , THR A:137 , GLN A:138 , GLU A:156 , THR A:158 , GLY A:160 , ARG A:163binding site for residue G5A A 300
2AC2SOFTWARETHR B:33 , ARG B:58 , ASP B:61 , ASN B:69 , ARG B:70 , LEU B:71 , TYR B:74 , GLN B:76 , TRP B:115 , GLU B:135 , ILE B:136 , THR B:137 , GLN B:138 , GLU B:156 , THR B:158 , GLY B:160 , ARG B:163 , HOH B:402binding site for residue G5A B 300
3AC3SOFTWARETHR C:33 , ARG C:58 , ASP C:61 , ASN C:69 , ARG C:70 , LEU C:71 , TYR C:74 , GLN C:76 , TRP C:115 , GLU C:135 , ILE C:136 , THR C:137 , GLN C:138 , GLU C:156 , THR C:158 , GLY C:160 , ARG C:163binding site for residue G5A C 300
4AC4SOFTWARETHR D:33 , ARG D:58 , ASP D:61 , ASN D:69 , ARG D:70 , LEU D:71 , TYR D:74 , GLN D:76 , TRP D:115 , GLU D:135 , ILE D:136 , THR D:137 , GLN D:138 , GLU D:156 , THR D:158 , GLY D:160 , ARG D:163binding site for residue G5A D 300
5AC5SOFTWARETHR E:33 , ARG E:58 , ASP E:61 , ASN E:69 , ARG E:70 , LEU E:71 , TYR E:74 , GLN E:76 , TRP E:115 , GLU E:135 , ILE E:136 , THR E:137 , GLN E:138 , GLU E:156 , THR E:158 , GLY E:160 , ARG E:163binding site for residue G5A E 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F5W)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Lys A:82 -Pro A:83
2Lys B:82 -Pro B:83
3Lys C:82 -Pro C:83
4Lys D:82 -Pro D:83
5Lys E:82 -Pro E:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F5W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F5W)

(-) Exons   (0, 0)

(no "Exon" information available for 5F5W)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..ee.........hhhhhhhhhh.......eeeeeeeeee.hhhh..........eeeeeeeeee....hhhhhhhhhhhhh..hhhhh.eeeeeeeeeehhhheeeeeeeeee..eeeeeeeeeeee..ee.....eeeeeehhhhhhhhh...hhhh.eee..eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f5w A   1 MYFQDIIMTLHKFWAEKGCLIWQPYDVEVGAGTMNPATFLKVLGKKPWNVAYVEPSRRPQDGRYGENPNRLQHYYQFQVILKPAPRNPQEIYLESLERLGINPLEHDIRFVEDDWESPTLGAWGLGWEVWLDGMEITQFTYFQQAGGLDLDEISVEITYGLERIAMYIQDKDSVFDIEWKEGITYGEIFKRSEWEWSKYNFELADTDMLFQVYEMFEKESKRMVEEGLIFPAYDYLLKCSHVFNILDARGAISVQERARYIRRMNNLAREIAKLYLQVFENVG 283
                                    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   


Chain B from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..ee.........hhhhhhhhhh.......eeeeeeeeee.hhhh..........eeeeeeeeee....hhhhhhhhhhhhh..hhhhh.eeeeeeeeeehhhheeeeeeeeee..eeeeeeeeeeee..ee.....eeeeeehhhhhhhhh........eee..eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f5w B   1 MYFQDIIMTLHKFWAEKGCLIWQPYDVEVGAGTMNPATFLKVLGKKPWNVAYVEPSRRPQDGRYGENPNRLQHYYQFQVILKPAPRNPQEIYLESLERLGINPLEHDIRFVEDDWESPTLGAWGLGWEVWLDGMEITQFTYFQQAGGLDLDEISVEITYGLERIAMYIQDKDSVFDIEWKEGITYGEIFKRSEWEWSKYNFELADTDMLFQVYEMFEKESKRMVEEGLIFPAYDYLLKCSHVFNILDARGAISVQERARYIRRMNNLAREIAKLYLQVFEN 281
                                    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 


Chain C from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..ee.........hhhhhhhhhhhhh....eeeeeeeeee.hhhh..........eeeeeeeeee....hhhhhhhhhhhhh..hhhhh.eeeeeeeeeehhhheeeeeeeeee..eeeeeeeeeeee..ee.....eeeeeehhhhhhhhh...hhhh.eee..eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f5w C   1 MYFQDIIMTLHKFWAEKGCLIWQPYDVEVGAGTMNPATFLKVLGKKPWNVAYVEPSRRPQDGRYGENPNRLQHYYQFQVILKPAPRNPQEIYLESLERLGINPLEHDIRFVEDDWESPTLGAWGLGWEVWLDGMEITQFTYFQQAGGLDLDEISVEITYGLERIAMYIQDKDSVFDIEWKEGITYGEIFKRSEWEWSKYNFELADTDMLFQVYEMFEKESKRMVEEGLIFPAYDYLLKCSHVFNILDARGAISVQERARYIRRMNNLAREIAKLYLQVFEN 281
                                    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 


Chain D from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..ee.........hhhhhhhhhh.......eeeeeeeeee.hhhh..........eeeeeeeeee....hhhhhhhhhhhhh..hhhhh.eeeeeeeeeehhhheeeeeeeeee..eeeeeeeeeeee..ee.....eeeeeehhhhhhhhhh.......eee..eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f5w D   3 FQDIIMTLHKFWAEKGCLIWQPYDVEVGAGTMNPATFLKVLGKKPWNVAYVEPSRRPQDGRYGENPNRLQHYYQFQVILKPAPRNPQEIYLESLERLGINPLEHDIRFVEDDWESPTLGAWGLGWEVWLDGMEITQFTYFQQAGGLDLDEISVEITYGLERIAMYIQDKDSVFDIEWKEGITYGEIFKRSEWEWSKYNFELADTDMLFQVYEMFEKESKRMVEEGLIFPAYDYLLKCSHVFNILDARGAISVQERARYIRRMNNLAREIAKLYLQVFE 280
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272        


Chain E from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..ee.........hhhhhhhhhh.......eeeeeeeeee.hhhh..........eeeeeeeeee....hhhhhhhhhhhhh..hhhhh.eeeeeeeeeehhhheeeeeeeeee..eeeeeeeeeeee..ee.....eeeeeehhhhhhhhh...hhhh.eee..eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f5w E   3 FQDIIMTLHKFWAEKGCLIWQPYDVEVGAGTMNPATFLKVLGKKPWNVAYVEPSRRPQDGRYGENPNRLQHYYQFQVILKPAPRNPQEIYLESLERLGINPLEHDIRFVEDDWESPTLGAWGLGWEVWLDGMEITQFTYFQQAGGLDLDEISVEITYGLERIAMYIQDKDSVFDIEWKEGITYGEIFKRSEWEWSKYNFELADTDMLFQVYEMFEKESKRMVEEGLIFPAYDYLLKCSHVFNILDARGAISVQERARYIRRMNNLAREIAKLYLQVFE 280
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
   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 5F5W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F5W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F5W)

(-) Gene Ontology  (9, 9)

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