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(-) Description

Title :  CRYSTAL STRUCTURE OF VIBH, AN NRPS CONDENSATION ENZYME
 
Authors :  T. A. Keating, C. G. Marshall, C. T. Walsh, A. E. Keating
Date :  06 Mar 02  (Deposition) - 26 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Nonribosomal Peptide Synthetase, Nrps Condensation Domain, Amide Synthase, Vibriobactin, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Keating, C. G. Marshall, C. T. Walsh, A. E. Keating
The Structure Of Vibh Represents Nonribosomal Peptide Synthetase Condensation, Cyclization And Epimerization Domains.
Nat. Struct. Biol. V. 9 522 2002
PubMed-ID: 12055621
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMIDE SYNTHASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET29B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VIBH
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Synonym: VIBH

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1L5A)

(-) Sites  (0, 0)

(no "Site" information available for 1L5A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L5A)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:331 -Pro A:332
2Ser B:331 -Pro B:332
3Ser C:331 -Pro C:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L5A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L5A)

(-) Exons   (0, 0)

(no "Exon" information available for 1L5A)

(-) 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:424
 aligned with Q9KTV9_VIBCH | Q9KTV9 from UniProtKB/TrEMBL  Length:438

    Alignment length:424
                                    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       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422    
         Q9KTV9_VIBCH     3 MLLAQKPFWQRHLAYPHINLDTVAHSLRLTGPLDTTLLLRALHLTVSEIDLFRARFSAQGELYWHPFSPPIDYQDLSIHLEAEPLAWRQIEQDLQRSSTLIDAPITSHQVYRLSHSEHLIYTRAHHIVLDGYGMMLFEQRLSQHYQSLLSGQTPTAAFKPYQSYLEEEAAYLTSHRYWQDKQFWQGYLREAPDLTLTSATYDPQLSHAVSLSYTLNSQLNHLLLKLANANQIGWPDALVALCALYLESAEPDAPWLWLPFMNRWGSVAANVPGLMVNSLPLLRLSAQQTSLGNYLKQSGQAIRSLYLHGRYRIEQIEQDQGLNAEQSYFMSPFINILPFESPHFADCQTELKVLASGSAEGINFTFRGSPQHELCLDITADLASYPQSHWQSHCERFPRFFEQLLARFQQVEQDVARLLAEPAA 426
               SCOP domains d1l5aa1 A:1-174 VibH                                                                                                                                                          d1l5aa2 A:175-424 VibH                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh......eeeeeeeee...hhhhhhhhhhhhhhhhhhh.eee.....eee.......eeee.....hhhhhhhhhhhhhhh...........eeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh.eeeeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhh.....eeeeee.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhh............eeeee..........eeeeeeeee.....eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l5a A   1 MLLAQKPFWQRHLAYPHINLDTVAHSLRLTGPLDTTLLLRALHLTVSEIDLFRARFSAQGELYWHPFSPPIDYQDLSIHLEAEPLAWRQIEQDLQRSSTLIDAPITSHQVYRLSHSEHLIYTRAHHIVLDGYGMMLFEQRLSQHYQSLLSGQTPTAAFKPYQSYLEEEAAYLTSHRYWQDKQFWQGYLREAPDLTLTSATYDPQLSHAVSLSYTLNSQLNHLLLKLANANQIGWPDALVALCALYLESAEPDAPWLWLPFMNRWGSVAANVPGLMVNSLPLLRLSAQQTSLGNYLKQSGQAIRSLYLHGRYRIEQIEQDQGLNAEQSYFMSPFINILPFESPHFADCQTELKVLASGSAEGINFTFRGSPQHELCLDITADLASYPQSHWQSHCERFPRFFEQLLARFQQVEQDVARLLAEPAA 424
                                    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       360       370       380       390       400       410       420    


Chain B from PDB  Type:PROTEIN  Length:424
 aligned with Q9KTV9_VIBCH | Q9KTV9 from UniProtKB/TrEMBL  Length:438

    Alignment length:424
                                    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       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422    
         Q9KTV9_VIBCH     3 MLLAQKPFWQRHLAYPHINLDTVAHSLRLTGPLDTTLLLRALHLTVSEIDLFRARFSAQGELYWHPFSPPIDYQDLSIHLEAEPLAWRQIEQDLQRSSTLIDAPITSHQVYRLSHSEHLIYTRAHHIVLDGYGMMLFEQRLSQHYQSLLSGQTPTAAFKPYQSYLEEEAAYLTSHRYWQDKQFWQGYLREAPDLTLTSATYDPQLSHAVSLSYTLNSQLNHLLLKLANANQIGWPDALVALCALYLESAEPDAPWLWLPFMNRWGSVAANVPGLMVNSLPLLRLSAQQTSLGNYLKQSGQAIRSLYLHGRYRIEQIEQDQGLNAEQSYFMSPFINILPFESPHFADCQTELKVLASGSAEGINFTFRGSPQHELCLDITADLASYPQSHWQSHCERFPRFFEQLLARFQQVEQDVARLLAEPAA 426
               SCOP domains d1l5ab1 B:1-174 VibH                                                                                                                                                          d1l5ab2 B:175-424 VibH                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh......eeeeeeeee...hhhhhhhhhhhhhhhhhhh.eee.....eee.......eeee.....hhhhhhhhhhhhhhh..........eeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh.eeeeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhh.....eeeeee.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh............eeeee..........eeeeeeeee.....eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l5a B   1 MLLAQKPFWQRHLAYPHINLDTVAHSLRLTGPLDTTLLLRALHLTVSEIDLFRARFSAQGELYWHPFSPPIDYQDLSIHLEAEPLAWRQIEQDLQRSSTLIDAPITSHQVYRLSHSEHLIYTRAHHIVLDGYGMMLFEQRLSQHYQSLLSGQTPTAAFKPYQSYLEEEAAYLTSHRYWQDKQFWQGYLREAPDLTLTSATYDPQLSHAVSLSYTLNSQLNHLLLKLANANQIGWPDALVALCALYLESAEPDAPWLWLPFMNRWGSVAANVPGLMVNSLPLLRLSAQQTSLGNYLKQSGQAIRSLYLHGRYRIEQIEQDQGLNAEQSYFMSPFINILPFESPHFADCQTELKVLASGSAEGINFTFRGSPQHELCLDITADLASYPQSHWQSHCERFPRFFEQLLARFQQVEQDVARLLAEPAA 424
                                    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       360       370       380       390       400       410       420    


Chain C from PDB  Type:PROTEIN  Length:424
 aligned with Q9KTV9_VIBCH | Q9KTV9 from UniProtKB/TrEMBL  Length:438

    Alignment length:424
                                    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       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422    
         Q9KTV9_VIBCH     3 MLLAQKPFWQRHLAYPHINLDTVAHSLRLTGPLDTTLLLRALHLTVSEIDLFRARFSAQGELYWHPFSPPIDYQDLSIHLEAEPLAWRQIEQDLQRSSTLIDAPITSHQVYRLSHSEHLIYTRAHHIVLDGYGMMLFEQRLSQHYQSLLSGQTPTAAFKPYQSYLEEEAAYLTSHRYWQDKQFWQGYLREAPDLTLTSATYDPQLSHAVSLSYTLNSQLNHLLLKLANANQIGWPDALVALCALYLESAEPDAPWLWLPFMNRWGSVAANVPGLMVNSLPLLRLSAQQTSLGNYLKQSGQAIRSLYLHGRYRIEQIEQDQGLNAEQSYFMSPFINILPFESPHFADCQTELKVLASGSAEGINFTFRGSPQHELCLDITADLASYPQSHWQSHCERFPRFFEQLLARFQQVEQDVARLLAEPAA 426
               SCOP domains d1l5ac1 C:1-174 VibH                                                                                                                                                          d1l5ac2 C:175-424 VibH                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Condensation-1l5aC01 C:1-283                                                                                                                                                                                                                                                               --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Condensation-1l5aC02 C:1-283                                                                                                                                                                                                                                                               --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) Condensation-1l5aC03 C:1-283                                                                                                                                                                                                                                                               --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhh......eeeeeeeee...hhhhhhhhhhhhhhhhhhh.eee.....eee.......eeee.....hhhhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh.ee......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhh.....eeeeee.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhh............eeeee..........eeeeeeee......eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l5a C   1 MLLAQKPFWQRHLAYPHINLDTVAHSLRLTGPLDTTLLLRALHLTVSEIDLFRARFSAQGELYWHPFSPPIDYQDLSIHLEAEPLAWRQIEQDLQRSSTLIDAPITSHQVYRLSHSEHLIYTRAHHIVLDGYGMMLFEQRLSQHYQSLLSGQTPTAAFKPYQSYLEEEAAYLTSHRYWQDKQFWQGYLREAPDLTLTSATYDPQLSHAVSLSYTLNSQLNHLLLKLANANQIGWPDALVALCALYLESAEPDAPWLWLPFMNRWGSVAANVPGLMVNSLPLLRLSAQQTSLGNYLKQSGQAIRSLYLHGRYRIEQIEQDQGLNAEQSYFMSPFINILPFESPHFADCQTELKVLASGSAEGINFTFRGSPQHELCLDITADLASYPQSHWQSHCERFPRFFEQLLARFQQVEQDVARLLAEPAA 424
                                    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       360       370       380       390       400       410       420
   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  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1L5A)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: CoA-acyltrans (22)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q9KTV9_VIBCH | Q9KTV9)
molecular function
    GO:0016880    acid-ammonia (or amide) ligase activity    Catalysis of the ligation of an acid to ammonia (NH3) or an amide via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
biological process
    GO:0019290    siderophore biosynthetic process    The chemical reactions and pathways resulting in the formation of siderophores, low molecular weight Fe(III)-chelating substances made by aerobic or facultatively anaerobic bacteria, especially when growing under iron deficient conditions. The complexes of Fe(3+)-siderophores have very high stability constants and are taken up by specific transport systems by microorganisms; the subsequent release of iron requires enzymatic action.

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  Cis Peptide Bonds
    Ser A:331 - Pro A:332   [ RasMol ]  
    Ser B:331 - Pro B:332   [ RasMol ]  
    Ser C:331 - Pro C:332   [ RasMol ]  
 

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  1l5a
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 Related Entries

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