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(-) Description

Title :  CRYSTAL STRUCTURE OF THE F-A DOMAINS OF THE LGRA INITIATION MODULE SOAKED WITH FON, AMPCPP, AND VALINE.
 
Authors :  J. M. Reimer, M. N. Aloise, T. M. Schmeing
Date :  16 Nov 15  (Deposition) - 20 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym./Biol. Unit :  A
Keywords :  Nrps, Formylation Domain, Adenylation Domain, Initiation Module, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Reimer, M. N. Aloise, P. M. Harrison, T. M. Schmeing
Synthetic Cycle Of The Initiation Module Of A Formylating Nonribosomal Peptide Synthetase.
Nature V. 529 239 2016
PubMed-ID: 26762462  |  Reference-DOI: 10.1038/NATURE16503

(-) Compounds

Molecule 1 - LINEAR GRAMICIDIN SYNTHETASE SUBUNIT A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-684
    Gene: LGRA
    Organism Scientific: BREVIBACILLUS PARABREVIS
    Organism Taxid: 54914

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2FON1Ligand/IonN-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
3VAL1Mod. Amino AcidVALINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:53 , TYR A:55 , ILE A:56 , LEU A:57 , ASN A:71 , ARG A:83 , ILE A:103 , ASP A:104 , HIS A:106 , VAL A:107 , ASP A:108 , PHE A:166 , LYS A:167 , ASP A:169 , HOH A:862binding site for residue FON A 701
2AC2SOFTWAREASP A:396 , TYR A:439 , GLY A:482 , ILE A:488 , APC A:703binding site for residue VAL A 702
3AC3SOFTWAREGLY A:463 , ASP A:464 , VAL A:465 , GLY A:480 , TYR A:481 , ILE A:504 , ASP A:568 , PHE A:580 , VAL A:702binding site for residue APC A 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ES7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:77 -Pro A:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ES7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ES7)

(-) Exons   (0, 0)

(no "Exon" information available for 5ES7)

(-) Sequences/Alignments

Asymmetric/Biological 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:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhh..eeeee.......hhhhh...eeeee......hhhhhhhh...eeeee.......ee.hhhhhhhhh....eeeeee.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.............eehhhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeee...hhhhhh...eeee..hhhhh...............eeeeee....eeeeehhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh......eeee..............eeeeee.hhhhh...eeee...........ee...eeeeee............eeeeeee.....ee..hhhhhhhheee......eeeeeeeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5es7 A   1 MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDV 702
                                    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       310       320       330       340       350 ||    365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585|
                                                                                                                                                                                                                                                                                                                                                                                         352|                                                                                                                                                                                                                                585|
                                                                                                                                                                                                                                                                                                                                                                                          358                                                                                                                                                                                                                                 702
   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  (0, 0)

(no "SCOP Domain" information available for 5ES7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ES7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ES7)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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    Leu A:77 - Pro A:78   [ RasMol ]  
 

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  LGRA_BREPA | Q70LM7
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 Related Entries

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

UniProtKB/Swiss-Prot
        LGRA_BREPA | Q70LM7: 5es5 5es6 5es8 5es9 5jnf

(-) Related Entries Specified in the PDB File

5es5 5ES5 CONTAINS A LONGER CONSTRUCT OF THE PROTEIN, LGRA, SHOWING THE FULL ADENYLATION DOMAIN WITH THE PEPTIDYL CARRIER PROTEIN BEING DISORDERED.
5es6 5ES6 CONTAINS THE PROTEIN WITHOUT SUBSTRATES.
5es8 5ES8 CONTAINS A LONGER CONSTRUCT OF THE PROTEIN, LGRA, SHOWING THE PEPTIDYL CARRIER PROTEIN IN THE THIOLATION STATE.
5es9 5ES9 CONTAINS A LONGER CONSTRUCT OF THE PROTEIN, LGRA, SHOWING THE PEPTIDYL CARRIER PROTEIN IN THE FORMYLATION STATE.