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(-) Description

Title :  FIREFLY LUCIFERASE INHIBITOR COMPLEX
 
Authors :  S. Lovell, K. P. Battaile, D. S. Auld, N. Thorne, W. A. Lea, D. J. Maloney, M. Shen, G. Raj, C. J. Thomas, A. Simeonov, R. P. Hanzlik, J. Inglese
Date :  23 Jul 09  (Deposition) - 16 Feb 10  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Monooxygenase, Photoprotein, Luminescence, Atp-Binding, Magnesium, Metal-Binding, Nucleotide-Binding, Peroxisome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. S. Auld, S. Lovell, N. Thorne, W. A. Lea, D. J. Maloney, M. Shen, G. Rai, K. P. Battaile, C. J. Thomas, A. Simeonov, R. P. Hanzlik, J. Inglese
Molecular Basis For The High-Affinity Binding And Stabilization Of Firefly Luciferase By Ptc124.
Proc. Natl. Acad. Sci. Usa V. 107 4878 2010
PubMed-ID: 20194791  |  Reference-DOI: 10.1073/PNAS.0909141107

(-) Compounds

Molecule 1 - LUCIFERIN 4-MONOOXYGENASE
    Chains: A
    EC Number: 1.13.12.7
    Organism Common: NORTH AMERICAN FIREFLY
    Organism Scientific: PHOTINUS PYRALIS
    Organism Taxid: 7054
    Synonym: LUCIFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1M241Ligand/Ion5'-O-[(R)-[({3-[5-(2-FLUOROPHENYL)-1,2,4-OXADIAZOL-3-YL]PHENYL}CARBONYL)OXY](HYDROXY)PHOSPHORYL]ADENOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:245 , PHE A:247 , 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 , THR A:346 , SER A:347 , ALA A:348 , VAL A:362 , ASP A:422 , ARG A:437 , HOH A:627 , HOH A:633 , HOH A:778BINDING SITE FOR RESIDUE M24 A 552

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMP_BINDINGPS00455 Putative AMP-binding domain signature.LUCI_PHOPY195-206  1A:195-206

(-) Exons   (0, 0)

(no "Exon" information available for 3IES)

(-) 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:431
 aligned with LUCI_PHOPY | P08659 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:436
                                    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       432      
           LUCI_PHOPY     3 DAKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPANDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSSGSTGLPKGVALPHRTACVRFSHARDPIFGNQIIPDTAILSVVPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSLQDYKIQSALLVPTLFSFFAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPEGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRL 438
               SCOP domains d3iesa_ A: Luciferase                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhee...........hhhhhhhhhhhhhhh....eeeee.....eeehhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...hhhhhhhhhh......eeee...........hhhhhhhhhh...................eeeeee.-----...eeeeehhhhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeeehhhhhhhhhhh.hhhhh......eeeee....hhhhhhhhhhhh.....eeeee.hhhh.eeee............ee....eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ies A   3 DAKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPANDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNS-----LPKGVALPHRTACVRFSHARDPIFGNQIIPDTAILSVVPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSLQDYKIQSALLVPTLFSFFAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPEGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRL 438
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     |   - |     212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432      
                                                                                                                                                                                                                             198   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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LUCI_PHOPY | P08659)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0047077    Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity    Catalysis of the reaction: O2 + ATP + Photinus luciferin = light + diphosphate + AMP + CO2 + oxidized Photinus luciferin.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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  3ies
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  LUCI_PHOPY | P08659
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  1.13.12.7
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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 3rix 4e5d 4g36 4g37 5dv9 5dwv 5kyt 5kyv

(-) Related Entries Specified in the PDB File

3iep FIREFLY LUCIFERASE SPO STRUCTURE (P41 FORM)
3ier FIREFLY LUCIFERASE APO STRUCTURE (P41 FORM) WITH PEG 400 BOUND