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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THERMOSTABLE JAPANESE FIREFLY LUCIFERASE RED-COLOR EMISSION S286N MUTANT COMPLEXED WITH HIGH-ENERGY INTERMEDIATE ANALOGUE
 
Authors :  T. Nakatsu, S. Ichiyama, J. Hiratake, A. Saldanha, N. Kobashi, K. Sakata, H. Kato, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  31 Aug 05  (Deposition) - 21 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta, Beta Barrel, Alpha+Beta, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nakatsu, S. Ichiyama, J. Hiratake, A. Saldanha, N. Kobashi, K. Sakata, H. Kato
Structural Basis For The Spectral Difference In Luciferase Bioluminescence.
Nature V. 440 372 2006
PubMed-ID: 16541080  |  Reference-DOI: 10.1038/NATURE04542
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LUCIFERIN 4-MONOOXYGENASE
    Chains: A
    EC Number: 1.13.12.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18
    Expression System Strain: HB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: JAPANESE FIREFLY
    Organism Scientific: LUCIOLA CRUCIATA
    Organism Taxid: 7051
    Synonym: LUCIFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3SLU1Ligand/Ion5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:201 , GLY A:527 , LEU A:528 , THR A:529 , GLY A:530 , LYS A:531BINDING SITE FOR RESIDUE CL A 1001
2AC2SOFTWARESER A:201 , GLY A:202 , GLY A:527 , LEU A:528 , HOH A:2139BINDING SITE FOR RESIDUE CL A 1002
3AC3SOFTWARESER A:200 , SER A:201 , HIS A:247 , PHE A:249 , THR A:253 , ILE A:288 , GLY A:318 , ALA A:319 , PRO A:320 , GLN A:340 , GLY A:341 , TYR A:342 , GLY A:343 , LEU A:344 , THR A:345 , ALA A:350 , ASP A:424 , ARG A:439 , LYS A:531 , HOH A:2002 , HOH A:2007 , HOH A:2099 , HOH A:2101 , HOH A:2172 , HOH A:2537BINDING SITE FOR RESIDUE SLU A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D1T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D1T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D1T)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMP_BINDINGPS00455 Putative AMP-binding domain signature.LUCI_LUCCR197-208  1A:197-208

(-) Exons   (0, 0)

(no "Exon" information available for 2D1T)

(-) 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:539
 aligned with LUCI_LUCCR | P13129 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:539
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536         
           LUCI_LUCCR     7 DENIVVGPKPFYPIEEGSAGTQLRKYMERYAKLGAIAFTNAVTGVDYSYAEYLEKSCCLGKALQNYGLVVDGRIALCSENCEEFFIPVIAGLFIGVGVAPTNEIYTLRELVHSLGISKPTIVFSSKKGLDKVITVQKTVTTIKTIVILDSKVDYRGYQCLDTFIKRNTPPGFQASSFKTVEVDRKEQVALIMNSSGSTGLPKGVQLTHENTVTRFSHARDPIYGNQVSPGTAVLTVVPFHHGFGMFTTLGYLICGFRVVMLTKFDEETFLKTLQDYKCTSVILVPTLFAILNKSELLNKYDLSNLVEIASGGAPLSKEVGEAVARRFNLPGVRQGYGLTETTSAIIITPEGDDKPGASGKVVPLFKAKVIDLDTKKSLGPNRRGEVCVKGPMLMKGYVNNPEATKELIDEEGWLHTGDIGYYDEEKHFFIVDRLKSLIKYKGYQVPPAELESVLLQHPSIFDAGVAGVPDPVAGELPGAVVVLESGKNMTEKEVMDYVASQVSNAKRLRGGVRFVDEVPKGLTGKIDGRAIREILKKPV 545
               SCOP domains d2d1ta_ A: Luciferase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...........hhhhhhhhhhhhhhhhh.eeeee.....eeehhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh....eeee...........hhhhhhhhh.....hhhhh..........eeeee...........eeeehhhhhhhhhhhh............eeee.....hhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhh...eeeehhhhhhhhhhh.hhhhh......eeeee....hhhhhhhhhhhh.....eeeee.hhhh.eeee............ee....eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee.hhh........hhhhhhhhhhh...eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhh..hhhhh....eee............hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1t A   7 DENIVVGPKPFYPIEEGSAGTQLRKYMERYAKLGAIAFTNAVTGVDYSYAEYLEKSCcLGKALQNYGLVVDGRIALCSENCEEFFIPVIAGLFIGVGVAPTNEIYTLRELVHSLGISKPTIVFSSKKGLDKVITVQKTVTTIKTIVILDSKVDYRGYQCLDTFIKRNTPPGYQASSFKTVEVDRKEQVALIMNSSGSTGLPKGVQLTHENIVTRFSHARDPIYGNQVSPGTAVLTVVPFHHGFGMFTTLGYLICGFRVVMLTKFDEETFLKTLQDYKCTNVILVPTLFAILNKSELLNKYDLSNLVEIASGGAPLSKEVGEAVARRFNLPGVRQGYGLTETTSAIIITPEGDDKPGASGKVVPLFKAKVIDLDTKKSLGPNRRGEVCVKGPMLMKGYVNNPEATKELIDEEGWLHTGDIGYYDEEKHFFIVDRLKSLIKYKGYQVPPAELESVLLQHPSIFDAGVAGVPDPVAGELPGAVVVLESGKNMTEKEVMDYVASQVSNAKRLRGGVRFVDEVPKGLTGKIDGRAIREILKKPV 545
                                    16        26        36        46        56       |66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536         
                                                                                    64-CSO
   Legend:   → Mismatch (orange background)
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  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 2D1T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D1T)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LUCI_LUCCR | P13129)
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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  2d1t
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 Related Entries

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

UniProtKB/Swiss-Prot
        LUCI_LUCCR | P13129: 2d1q 2d1r 2d1s

(-) Related Entries Specified in the PDB File

2d1r T217I MUTANT WITH OLU
2d1s T217I MUTANT WITH SLU RELATED ID: MY_001000084.4 RELATED DB: TARGETDB