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(-) Description

Title :  STRUCTURE OF PHOTINUS PYRALIS LUCIFERASE RED LIGHT EMITTING VARIANT
 
Authors :  A. M. Gulick
Date :  22 Jul 16  (Deposition) - 21 Dec 16  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Adenylation Forming Enzyme, Ligase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. R. Branchini, T. L. Southworth, D. M. Fontaine, M. H. Murtiashaw, A. Mcgurk, M. H. Talukder, R. Qureshi, D. Yetil, J. A. Sundlov, A. M. Gulick
Cloning Of The Orange Light-Producing Luciferase From Photinus Scintillans-A New Proposal On How Bioluminescence Color Is Determined.
Photochem. Photobiol. V. 93 479 2017
PubMed-ID: 27861940  |  Reference-DOI: 10.1111/PHP.12671

(-) Compounds

Molecule 1 - LUCIFERIN 4-MONOOXYGENASE
    ChainsA, B
    EC Number1.13.12.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    MutationYES
    Organism CommonCOMMON EASTERN FIREFLY
    Organism ScientificPHOTINUS PYRALIS
    Organism Taxid7054
    SynonymLUCIFERASE

 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, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2SLU2Ligand/Ion5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SLU1Ligand/Ion5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2SLU1Ligand/Ion5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:245 , PHE A:247 , THR A:251 , 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 , ALA A:348 , VAL A:362 , ASP A:422 , ARG A:437 , LYS A:529 , HOH A:784 , HOH A:792 , HOH A:816 , HOH A:927 , HOH A:940binding site for residue SLU A 601
2AC2SOFTWAREGLN A:134 , ASP A:413 , ASP A:415 , HOH A:823 , HOH A:835binding site for residue EDO A 602
3AC3SOFTWAREHIS B:245 , PHE B:247 , THR B:251 , 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 , ALA B:348 , ASP B:422 , ARG B:437 , LYS B:529 , HOH B:801 , HOH B:859 , HOH B:877 , HOH B:923 , HOH B:926 , HOH B:952 , HOH B:961binding site for residue SLU B 601
4AC4SOFTWAREGLU B:18 , ASP B:19 , LYS B:28binding site for residue EDO B 602
5AC5SOFTWAREILE A:231 , TYR B:15 , ARG B:32 , TYR B:33 , ILE B:231 , ILE B:257 , HOH B:708binding site for residue EDO B 603
6AC6SOFTWAREILE B:192 , HOH B:901binding site for residue EDO B 604
7AC7SOFTWARELEU B:17 , ARG B:213 , PRO B:395 , HOH B:775binding site for residue EDO B 605
8AC8SOFTWAREHIS B:46 , ARG B:387 , TYR B:425 , HOH B:766binding site for residue EDO B 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KYT)

(-) 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:532
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...........hhhhhhhhhhhhhhh....eeeee....eeeehhhhhhhhhhhhhhhhhh......eeeee......hhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeee...hhhhhhhhhh......eeee...........hhhhhhhh......hhhhh..........eeeeee.........eeeeehhhhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeeehhhhhhhhhh..hhhhh......eeeee....hhhhhhhhhhhh.....eeeee.hhhh.eeee............ee....eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee.hhheee..eeehhhhhhhhhhh...eeeeeeee.....eeeeeeee...hhhhhhhhh..hhhhh...eeeee...........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kyt A   4 AKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPANDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSSGSTGLPKGVALPHRTACVRFSHARDPIFGNQIIPDTAILSVVPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSLQDYKIQTALLVPTLFSFFAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPEGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGYQVAPAELESILLQHPFDAGVAGLPDDDAGELPAAVVVLEEKEIVDYVASQVTTAKKLRGGVVFVDEVPKGLTGKLDARKIREILIKAK 543
                                    13        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       465       475       485  ||   501       511       521       531       541  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    462|                    488|                                                
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     465                     495                                                

Chain B from PDB  Type:PROTEIN  Length:543
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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....hhhhh..........eeeeeee...eeeeeehhhhhhhhhhhh............eeee.....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeeehhhhhhhhh...hhhhh......eeeee....hhhhhhhhhhhh.....eeeee.hhhh.eeee............ee....eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee.hhheee..eeehhhhhhhhhhhh..eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhh..hhhhh...eeee............hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kyt B   4 AKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPANDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSSLPKGVALPHRTACVRFSHARDPIFGNQIIPDTAILSVVPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSLQDYKIQTALLVPTLFSFFAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPEGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGYQVAPAELESILLQHPNIFDAGVAGLPDDDAGELPAAVVVLEHGKTMTEKEIVDYVASQVTTAKKLRGGVVFVDEVPKGLTGKLDARKIREILIKAKKGGKSKL 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)
  - → 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 5KYT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | P086591ba3 1lci 3iep 3ier 3ies 3rix 4e5d 4g36 4g37 5dv9 5dwv 5kyv

(-) Related Entries Specified in the PDB File

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