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(-) Description

Title :  STRUCTURAL AND FUNCTIONAL STUDIES OF FATTY ACYL-ADENYLATE LIGASES FROM E. COLI AND L. PNEUMOPHILA
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  20 Oct 10  (Deposition) - 22 Dec 10  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Faal, Fatty Acid Amp Ligase, Atp-Dependent Amp-Binding Enzyme Family, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, R. Zhou, J. M. Sauder, P. J. Tonge, S. K. Burley, S. Swaminatha
Structural And Functional Studies Of Fatty Acyl Adenylate Ligases From E. Coli And L. Pneumophila.
J. Mol. Biol. V. 406 313 2011
PubMed-ID: 21185305  |  Reference-DOI: 10.1016/J.JMB.2010.12.011

(-) Compounds

Molecule 1 - FATTY ACYL-ADENYLATE LIGASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3) CODON+RIL STRATAGENE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: C3712
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 217992
    Strain: O6
    Synonym: PUTATIVE SAFRAMYCIN MX1 SYNTHETASE B

 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  (2, 19)

Asymmetric Unit (2, 19)
No.NameCountTypeFull Name
11ZZ2Ligand/Ion5'-O-[(S)-(DODECANOYLOXY)(HYDROXY)PHOSPHORYL]ADENOSINE
2MSE17Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
11ZZ1Ligand/Ion5'-O-[(S)-(DODECANOYLOXY)(HYDROXY)PHOSPHORYL]ADENOSINE
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
11ZZ1Ligand/Ion5'-O-[(S)-(DODECANOYLOXY)(HYDROXY)PHOSPHORYL]ADENOSINE
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:208 , ASP A:230 , GLY A:235 , ALA A:308 , GLU A:309 , PRO A:310 , CYS A:336 , TYR A:337 , GLY A:338 , LEU A:339 , ALA A:340 , LEU A:344 , ASP A:445 , VAL A:456 , ARG A:459 , SER A:549 , LYS A:551BINDING SITE FOR RESIDUE 1ZZ A 1
2AC2SOFTWAREILE B:208 , GLY B:235 , ALA B:308 , GLU B:309 , PRO B:310 , ILE B:311 , CYS B:336 , TYR B:337 , GLY B:338 , LEU B:339 , ALA B:340 , LEU B:344 , ASP B:445 , VAL B:456 , ARG B:459 , SER B:549 , LYS B:551 , HOH B:609BINDING SITE FOR RESIDUE 1ZZ B 585

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:541 -His A:542

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PBK)

(-) 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:555
 aligned with A0A0H2VDD9_E | A0A0H2VDD9 from UniProtKB/TrEMBL  Length:576

    Alignment length:555
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563     
         A0A0H2VDD9_E    14 PMRYADFPTLVDALDYAALSSAGMNFYDRRCQLEDQLEYQTLKARAEAGAKRLLSLNLKKGDRVALIAETSSEFVEAFFACQYAGLVAVPLAIPMGVGQRDSWSAKLQGLLASCQPAAIITGDEWLPLVNAATHDNPELHVLSHAWFKALPEADVALQRPVPNDIAYLQYTSGSTRFPRGVIITHREVMANLRAISHDGIKLRPGDRCVSWLPFYHDMGLVGFLLTPVATQLSVDYLRTQDFAMRPLQWLKLISKNRGTVSVAPPFGYELCQRRVNEKDLAELDLSCWRVAGIGAEPISAEQLHQFAECFRQVNFDNKTFMPCYGLAENALAVSFSDEASGVVVNEVDRDILEYQGKAVAPGAETRAVSTFVNCGKALPEHGIEIRNEAGMPVAERVVGHICISGPSLMSGYFGDQVSQDEIAATGWLDTGDLGYLLDGYLYVTGRIKDLIIIRGRNIWPQDIEYIAEQEPEIHSGDAIAFVTAQEKIILQIQCRISDEERRGQLIHALAARIQSEFGVTAAIDLLPPHSIPRTSSGKPARAEAKKRYQKAYAAS 568
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh....eeeee.....eeeeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh...eeeehhhhhh...............eeeee...........eeeehhhhhhhhhhhhhh.........eee.....hhhhhhhhhhhhhhh...eee.hhhhhhhh.hhhhhhhhhh...eeeehhhhhhhhhhh.hhhhhh........eeee.....hhhhhhhhhhhhhhhh.hhh.eeeeee.hhhh.eeee........eeeeehhhhhhhh...........eeeee...ee....eeeee............eeeeee..........hhhhhhhhhhhh.eeeeeeeeee..eeeeeee....eee..eeehhhhhhhhhh.........eeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pbk A  14 PmRYADFPTLVDALDYAALSSAGmNFYDRRCQLEDQLEYQTLKARAEAGAKRLLSLNLKKGDRVALIAETSSEFVEAFFACQYAGLVAVPLAIPmGVGQRDSWSAKLQGLLASCQPAAIITGDEWLPLVNAATHDNPELHVLSHAWFKALPEADVALQRPVPNDIAYLQYTSGSTRFPRGVIITHREVmANLRAISHDGIKLRPGDRCVSWLPFYHDmGLVGFLLTPVATQLSVDYLRTQDFAmRPLQWLKLISKNRGTVSVAPPFGYELCQRRVNEKDLAELDLSCWRVAGIGAEPISAEQLHQFAECFRQVNFDNKTFmPCYGLAENALAVSFSDEASGVVVNEVDRDILEYQGKAVAPGAETRAVSTFVNCGKALPEHGIEIRNEAGmPVAERVVGHICISGPSLmSGYFGDQVSQDEIAATGWLDTGDLGYLLDGYLYVTGRIKDLIIIRGRNIWPQDIEYIAEQEPEIHSGDAIAFVTAQEKIILQIQCRISDEERRGQLIHALAARIQSEFGVTAAIDLLPPHSIPRTSSGKPARAEAKKRYQKAYAAS 568
                             |      23        33   |    43        53        63        73        83        93       103    |  113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   |   263       273       283       293       303       313       323       333|      343       353       363       373       383       393       403|      413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563     
                             |                    37-MSE                                                                108-MSE                                                                                       202-MSE                      231-MSE                   257-MSE                                                                      334-MSE                                                               404-MSE           422-MSE                                                                                                                                              
                            15-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:550
 aligned with A0A0H2VDD9_E | A0A0H2VDD9 from UniProtKB/TrEMBL  Length:576

    Alignment length:557
                                    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       432       442       452       462       472       482       492       502       512       522       532       542       552       562       
         A0A0H2VDD9_E    13 LPMRYADFPTLVDALDYAALSSAGMNFYDRRCQLEDQLEYQTLKARAEAGAKRLLSLNLKKGDRVALIAETSSEFVEAFFACQYAGLVAVPLAIPMGVGQRDSWSAKLQGLLASCQPAAIITGDEWLPLVNAATHDNPELHVLSHAWFKALPEADVALQRPVPNDIAYLQYTSGSTRFPRGVIITHREVMANLRAISHDGIKLRPGDRCVSWLPFYHDMGLVGFLLTPVATQLSVDYLRTQDFAMRPLQWLKLISKNRGTVSVAPPFGYELCQRRVNEKDLAELDLSCWRVAGIGAEPISAEQLHQFAECFRQVNFDNKTFMPCYGLAENALAVSFSDEASGVVVNEVDRDILEYQGKAVAPGAETRAVSTFVNCGKALPEHGIEIRNEAGMPVAERVVGHICISGPSLMSGYFGDQVSQDEIAATGWLDTGDLGYLLDGYLYVTGRIKDLIIIRGRNIWPQDIEYIAEQEPEIHSGDAIAFVTAQEKIILQIQCRISDEERRGQLIHALAARIQSEFGVTAAIDLLPPHSIPRTSSGKPARAEAKKRYQKAYAASL 569
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh....eeeee.....eeeeeehhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhh..eeeee...-------hhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh.....eeeehhhhhhh..............eeeeehhhh.......eeeehhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhhh...hhh.eeeee.hhhhh...ee........eeeeehhhhhhhh...........eeeee...ee....eeeee............eeeeee......ee..hhhhhhhhhhhh.eeeeeeeeee..eeeeeee....ee....eehhhhhhhhhhh........eeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pbk B  13 LPmRYADFPTLVDALDYAALSSAGmNFYDRRCQLEDQLEYQTLKARAEAGAKRLLSLNLKKGDRVALIAETSSEFVEAFFACQYAGLVAVPLAIP-------SWSAKLQGLLASCQPAAIITGDEWLPLVNAATHDNPELHVLSHAWFKALPEADVALQRPVPNDIAYLQYTSGSTRFPRGVIITHREVmANLRAISHDGIKLRPGDRCVSWLPFYHDmGLVGFLLTPVATQLSVDYLRTQDFAmRPLQWLKLISKNRGTVSVAPPFGYELCQRRVNEKDLAELDLSCWRVAGIGAEPISAEQLHQFAECFRQVNFDNKTFmPCYGLAENALAVSFSDEASGVVVNEVDRDILEYQGKAVAPGAETRAVSTFVNCGKALPEHGIEIRNEAGmPVAERVVGHICISGPSLmSGYFGDQVSQDEIAATGWLDTGDLGYLLDGYLYVTGRIKDLIIIRGRNIWPQDIEYIAEQEPEIHSGDAIAFVTAQEKIILQIQCRISDEERRGQLIHALAARIQSEFGVTAAIDLLPPHSIPRTSSGKPARAEAKKRYQKAYAASL 569
                              |     22        32    |   42        52        62        72        82        92       102    |    -  |    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       432       442       452       462       472       482       492       502       512       522       532       542       552       562       
                             15-MSE                37-MSE                                                               107     115                                                                                    202-MSE                      231-MSE                   257-MSE                                                                      334-MSE                                                               404-MSE           422-MSE
   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 3PBK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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