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(-) Description

Title :  PHOTINUS PYRALIS LUCIFERASE IN THE ADENYLATE-FORMING CONFORMATION BOUND TO DLSA
 
Authors :  J. A. Sundlov, B. R. Branchini, A. M. Gulick
Date :  13 Jul 12  (Deposition) - 15 Aug 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Anl Superfamily, Ligase, Adenylating Enzymes, Luciferase, Domain Alternation, Firefly Luciferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Sundlov, D. M. Fontaine, T. L. Southworth, B. R. Branchini, A. M. Gulick
Crystal Structure Of Firefly Luciferase In A Second Catalytic Conformation Supports A Domain Alternation Mechanism.
Biochemistry V. 51 6493 2012
PubMed-ID: 22852753  |  Reference-DOI: 10.1021/BI300934S

(-) Compounds

Molecule 1 - LUCIFERIN 4-MONOOXYGENASE
    Chains: A, B
    EC Number: 1.13.12.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PGEX-6P-2
    Organism Common: NORTH AMERICAN FIREFLY
    Organism Scientific: PHOTINUS PYRALIS
    Organism Taxid: 7054
    Synonym: LUCIFERASE

 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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SLU2Ligand/Ion5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SLU1Ligand/Ion5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SLU1Ligand/Ion5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:245 , PHE A:247 , ALA A:313 , SER A:314 , GLY A:315 , GLY A:316 , ALA A:317 , PRO A:318 , GLN A:338 , GLY A:339 , TYR A:340 , GLY A:341 , LEU A:342 , THR A:343 , SER A:347 , ALA A:348 , VAL A:362 , ASP A:422 , ARG A:437 , LYS A:529 , HOH A:713 , HOH A:735BINDING SITE FOR RESIDUE SLU A 601
2AC2SOFTWAREHIS B:245 , PHE B:247 , THR B:251 , SER B:314 , GLY B:315 , GLY B:316 , ALA B:317 , PRO B:318 , GLN B:338 , GLY B:339 , TYR B:340 , GLY B:341 , LEU B:342 , THR B:343 , SER B:347 , ALA B:348 , VAL B:362 , ASP B:422 , ARG B:437 , LYS B:529BINDING SITE FOR RESIDUE SLU B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G36)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G36)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G36)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G36)

(-) Exons   (0, 0)

(no "Exon" information available for 4G36)

(-) 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:522
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4g36a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee...........hhhhhhhhhhhhhhh....eeeee....eeeehhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...hhhhhhhhhh......eeee...........hhhhhhhhhh...................eeeee......eeeehhhhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhh...eee.hhhhhhhhh..hhhhh.......eeeee....hhhhhhhhhhhh.....eeee.hhhhh...ee............ee....eeeee.............eeeeee......ee..hhhhhhh.......eeeeeeeee.....eeeeee.hhheee..eeehhhhhhhhhh.eeeeee.......eeeeee....hhhhhhhhhh..hhhhh....eee..............hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g36 A   4 AKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPANDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSLPKGVALPHRTACVRFSHARDPIFGNQIIPDTAILSVVPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSLQDYKIQSALLVPTLFSFFAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPEGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGYQVAPAELESILLDAGVAGLPDDDAGELPAAVVVLETEKEIVDYVASQVTTAKKLRGGVVFVDEVPKGLTGKLDARKIREILIK 541
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    || 208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458||     474       484   ||  499       509       519       529       539  
                                                                                                                                                                                                                            198|                                                                                                                                                                                                                                                            459|                   488|                                               
                                                                                                                                                                                                                             204                                                                                                                                                                                                                                                             466                    494                                               


Chain B from PDB  Type:PROTEIN  Length:543
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4g36b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...........hhhhhhhhhhhhhhh....eeeee....eeeehhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhh...eeeee....hhhhhhhhhhhhh..eeee...hhhhhhhhhh......eeee...........hhhhhhhhhh....hhhhh..........eeeeeee...eeeeeehhhhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhh.....eeeee.hhhh.eeee............ee....eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee.hhhee....eehhhhhhhhhhhh..eeeeeeeeee.....eeeeeeeee......hhhhhhhhhhh...........eee............hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g36 B   4 AKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPANDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSSLPKGVALPHRTACVRFSHARDPIFGNQIIPDTAILSVVPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSLQDYKIQSALLVPTLFSFFAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPEGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGYQVAPAELESILLQHPNIFDAGVAGLPDDDAGELPAAVVVLEHGKTMTEKEIVDYVASQVTTAKKLRGGVVFVDEVPKGLTGKLDARKIREILIKAKKGGKSKL 550
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193     ||207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547   
                                                                                                                                                                                                                             199|                                                                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                              204
   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  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G36)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G36)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LUCI_PHOPY | P08659: 1ba3 1lci 3iep 3ier 3ies 3rix 4e5d 4g37 5dv9 5dwv 5kyt 5kyv

(-) Related Entries Specified in the PDB File

1lci 2d1s 3iep 4g37