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(-) Description

Title :  THE THIRD ADENYLATION DOMAIN OF THE FUNGAL SIDN NON-RIBOSOMAL PEPTIDE SYNTHETASE
 
Authors :  T. V. Lee, J. S. Lott, R. D. Johnson, L. J. Johnson, V. L. Arcus
Date :  28 Aug 09  (Deposition) - 17 Nov 09  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase, Non-Ribosomal Peptide Synthesis, Nrps, Siderophore Synthetase, Sidna3, Fungal, Endophyte (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. V. Lee, L. J. Johnson, R. D. Johnson, A. Koulman, G. A. Lane, J. S. Lott V. L. Arcus
Structure Of A Eukaryotic Nonribosomal Peptide Synthetase Adenylation Domain That Activates A Large Hydroxamate Amino Acid In Siderophore Biosynthesis
J. Biol. Chem. V. 285 2415 2010
PubMed-ID: 19923209  |  Reference-DOI: 10.1074/JBC.M109.071324

(-) Compounds

Molecule 1 - SIDN SIDEROPHORE SYNTHETASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST17
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: THIRD ADENYLATION DOMAIN
    Gene: SIDN
    Organism Scientific: NEOTYPHODIUM LOLII
    Organism Taxid: 73839
    Strain: LP19

 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  (3, 22)

Asymmetric Unit (3, 22)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MSE18Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:83 , GLU A:105 , SER A:227 , ARG A:228 , ARG A:252 , HOH A:679BINDING SITE FOR RESIDUE SO4 A 558
2AC2SOFTWARESER A:18 , MSE A:95 , ASN A:165 , ARG A:192BINDING SITE FOR RESIDUE CL A 559
3AC3SOFTWAREARG B:83 , GLU B:105 , SER B:227 , ARG B:228 , ARG B:252 , HOH B:650 , HOH B:920BINDING SITE FOR RESIDUE SO4 B 558
4AC4SOFTWARESER B:18 , ASN B:165 , ARG B:192BINDING SITE FOR RESIDUE CL B 559

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ITE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ITE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ITE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ITE)

(-) Exons   (0, 0)

(no "Exon" information available for 3ITE)

(-) 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:402
 aligned with K7NCP5_EPIFI | K7NCP5 from UniProtKB/TrEMBL  Length:1928

    Alignment length:410
                                   639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039
        K7NCP5_EPIFI    630 STVPPSHYIETWAKTHPEWKAVEVATGFLGSQKIVTEDWTYKKLNETANQVANLIIHASLHGRAIAVSLDRSLIAFAIIVGIMKSGNTYVPIEAGLPNDRKSFLLRDSRAAMAFVCDNNFDGVELPPETKVLDTKNQSFIENLSTQDTSDILNNYPENLDAYLLYTSGSTGTPKGVRVSRHNLSSFSDAWGKLIGNVAPKSLELGGVGKFLCLASRAFDVHIGEMFLAWRFGLCAVTGERLSMLDDLPRTFRELGVTHAGIVPSLLDQTGLVPEDAPHLVYLGVGGEKMTPRTQQIWSSSDRVALVNVYGPTEVTIGCSAGRILPDSDTRCIGHPLGDSVAHVLAPGSNEHVKKGMAGELVIEGSLVANGYLNRPDAKGFCDINGRKMYRTGDIVRMDADSSILFLGRKD 1039
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh...eeeeeee..-----.eeeeeehhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee..............eeee..hhhhhhhhhhh.............eeeeeee.---...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...eeeehhhhhhhhh.hhhhh....eeeee....hhhhhhhhh.....eeeeee.hhhhh...eeee........eeeee....eeeee.............eeeeee......ee........eeee..eeeeeeeeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ite A   13 STVPPSHYIETWAKTHPEWKAVEVATGF-----IVTEDWTYKKLNETANQVANLIIHASLHGRAIAVSLDRSLIAFAIIVGImKSGNTYVPIEAGLPNDRKSFLLRDSRAAmAFVCDNNFDGVELPPETKVLDTKNQSFIENLSTQDTSDILNNYPENLDAYLLYTS---GTPKGVRVSRHNLSSFSDAWGKLIGNVAPKSLELGGVGKFLCLASRAFDVHIGEmFLAWRFGLCAVTGERLSmLDDLPRTFRELGVTHAGIVPSLLDQTGLVPEDAPHLVYLGVGGEKmTPRTQQIWSSSDRVALVNVYGPTEVTIGCSAGRILPDSDTRCIGHPLGDSVAHVLAPGSNEHVKKGmAGELVIEGSLVANGYLNRPDAKGFCDINGRKmYRTGDIVRmDADSSILFLGRKD  422
                                    22        32       | -   |    52        62        72        82        92  |    102       112       122 |     132       142       152       162       172      |  -|      192       202       212       222       232    |  242       252  |    262       272       282       292       302       312       322       332       342       352       362     | 372       382       392       402      |412       422
                                                      40    46                                               95-MSE                      124-MSE                                                179 183                                                   237-MSE           255-MSE                                       301-MSE                                                            368-MSE                         400-MSE  409-MSE         


Chain B from PDB  Type:PROTEIN  Length:503
 aligned with K7NCP5_EPIFI | K7NCP5 from UniProtKB/TrEMBL  Length:1928

    Alignment length:525
                                   638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148     
        K7NCP5_EPIFI    629 TSTVPPSHYIETWAKTHPEWKAVEVATGFLGSQKIVTEDWTYKKLNETANQVANLIIHASLHGRAIAVSLDRSLIAFAIIVGIMKSGNTYVPIEAGLPNDRKSFLLRDSRAAMAFVCDNNFDGVELPPETKVLDTKNQSFIENLSTQDTSDILNNYPENLDAYLLYTSGSTGTPKGVRVSRHNLSSFSDAWGKLIGNVAPKSLELGGVGKFLCLASRAFDVHIGEMFLAWRFGLCAVTGERLSMLDDLPRTFRELGVTHAGIVPSLLDQTGLVPEDAPHLVYLGVGGEKMTPRTQQIWSSSDRVALVNVYGPTEVTIGCSAGRILPDSDTRCIGHPLGDSVAHVLAPGSNEHVKKGMAGELVIEGSLVANGYLNRPDAKGFCDINGRKMYRTGDIVRMDADSSILFLGRKDEQVKVRGQRLELGEVSEVIRSLSPTDIDVVTLLLNHPGTSKQFLVSFVASSGAAVRGELRWINENYKEINNSLRQACEQTLPAYMVPDFIIPISFIPLRDTSAKTDAKALEHMF 1153
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh...eeeeeee..-----.eeeeeehhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee..............eeee..hhhhhhhhh...............eeeeeee..--...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...eeeehhhhhhhhh.hhhhh....eeeee....hhhhhhhhh.....eeeeee.hhhhh...eeee........eeeee....eeeee............eeeeeee......ee........eeee..eeeeeeeeeeee.....eeeeee......---...hhhhhhhhhhhhh...eeeeee..--------..eeeeee..........----...hhhhhhhhhhhhh.hhhhh...eee.............hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ite B   12 TSTVPPSHYIETWAKTHPEWKAVEVATGF-----IVTEDWTYKKLNETANQVANLIIHASLHGRAIAVSLDRSLIAFAIIVGImKSGNTYVPIEAGLPNDRKSFLLRDSRAAmAFVCDNNFDGVELPPETKVLDTKNQSFIENLSTQDTSDILNNYPENLDAYLLYTSG--GTPKGVRVSRHNLSSFSDAWGKLIGNVAPKSLELGGVGKFLCLASRAFDVHIGEmFLAWRFGLCAVTGERLSmLDDLPRTFRELGVTHAGIVPSLLDQTGLVPEDAPHLVYLGVGGEKmTPRTQQIWSSSDRVALVNVYGPTEVTIGCSAGRILPDSDTRCIGHPLGDSVAHVLAPGSNEHVKKGmAGELVIEGSLVANGYLNRPDAKGFCDINGRKmYRTGDIVRmDADSSILFLGRKDEQVK---QRLELGEVSEVIRSLSPTDIDVVTLLL--------FLVSFVASSGAAVRGELR----NYKEINNSLRQACEQTLPAYmVPDFIIPISFIPLRDTSAKTDAKALEHmF  536
                                    21        31        |-    |   51        61        71        81        91   |   101       111       121  |    131       141       151       161       171        |- |     191       201       211       221       231     | 241       251   |   261       271       281       291       301       311       321       331       341       351       361      |371       381       391       401       411       421    |  431       441       451    |    -   |   471       481|    | 491       501     | 511       521       531   | 
                                                       40    46                                               95-MSE                      124-MSE                                                 180  |                                                   237-MSE           255-MSE                                       301-MSE                                                            368-MSE                         400-MSE  409-MSE          426 430                       456      465              482  487                 507-MSE                     535-MSE
                                                                                                                                                                                                     183
   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 3ITE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ITE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ITE)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (K7NCP5_EPIFI | K7NCP5)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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