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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LGRA INITIATION MODULE IN THE FORMYLATION STATE
 
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 :  3.77
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nrps, Formylation Domain, Adenylation Domain, Peptidyl Carrier Protein, 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, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-766
    Gene: LGRA
    Organism Scientific: BREVIBACILLUS PARABREVIS
    Organism Taxid: 54914

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PNS1Ligand/Ion4'-PHOSPHOPANTETHEINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PNS1Ligand/Ion4'-PHOSPHOPANTETHEINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PNS-1Ligand/Ion4'-PHOSPHOPANTETHEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:728 , SER A:729binding site for residue PNS A 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ES9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ES9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ES9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ES9)

(-) Exons   (0, 0)

(no "Exon" information available for 5ES9)

(-) 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:759
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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.............ee.hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeee...hhhhhh...eeee..hhhhh...............eeeeeee...eeeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhh......eeee..............eeeeee.........eeee...........ee...eeeeee............eeeeeee.....ee..hhhhhhhheee......eeeeeeeeeee.....eee...............hhhhhhhhhhh.....eeeeeeee.....eeeeeeee.....hhhhhhhhhhh.........eeeee.............................hhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5es9 A   1 MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSLAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEIEPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDVQADAVAPTDELEQQLAQVWSHVLGIPQMGIDDHFLERGGDSIKVMQLIHQLKNIGLSLRYDQLFTHPTIRQLKRLLTEQAAA 770
                                    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 ||    364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684||     701       711       721       731       741       751       761         
                                                                                                                                                                                                                                                                                                                                                                                         352|                                                                                                                                                                                                                                                                                                                                     685|                                                                             
                                                                                                                                                                                                                                                                                                                                                                                          357                                                                                                                                                                                                                                                                                                                                      693                                                                             


Chain B from PDB  Type:PROTEIN  Length:681
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.............ee.hhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeee...hhhhhh...eeee......................eeeeeee...eeeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh..eee...hhhhhhh........eeeee.............eeeeee.hhhhh...eeeee..........ee...eeeeee............eeeeeee.....ee..hhhhhhhheee......eeeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhhh.....eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhh.......eeeee...........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5es9 B   1 MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSLAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEIEPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDVQADA 685
                                    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 ||    364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684 
                                                                                                                                                                                                                                                                                                                                                                                         352|                                                                                                                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                          357
   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 5ES9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ES9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ES9)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LGRA_BREPA | Q70LM7: 5es5 5es6 5es7 5es8 5jnf

(-) Related Entries Specified in the PDB File

5es5 5ES5 CONTAINS THE SAME CONSTRUCT PROTEIN WHERE THE PEPTIDYL CARRIER PROTEIN IS DISORDERED.
5es6 5ES6 CONTAINS A SHORTER CONSTRUCT OF THE PROTEIN THAT DOES NOT INCLUDE THE PEPTIDYL CARRIER PROTEIN.
5es7 5ES7 CONTAINS A SHORTER CONSTRUCT OF THE PROTEIN THAT DOES NOT INCLUDE THE PEPTIDYL CARRIER PROTEIN AND IS SOAKED WITH SUBSTRATES.
5es8 5ES8 CONTAINS THE SAME PROTEIN, BUT IN THE THIOLATION STATE CONFORMATION.