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(-) Description

Title :  X-RAY STRUCTURE OF GENETICALLY ENCODED PHOTOSENSITIZER KILLERRED IN NATIVE FORM
 
Authors :  S. Pletnev, N. V. Pletneva, V. Z. Pletnev
Date :  18 Feb 09  (Deposition) - 08 Sep 09  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fluorescent Protein, Genetically Encoded Photosensitizer, Killerred, Phototoxicity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pletnev, N. G. Gurskaya, N. V. Pletneva, K. A. Lukyanov, D. M. Chudakov, V. I. Martynov, V. O. Popov, M. V. Kovalchuk, A. Wlodawer, Z. Dauter, V. Pletnev
Structural Basis For Phototoxicity Of The Genetically Encoded Photosensitizer Killerred.
J. Biol. Chem. V. 284 32028 2009
PubMed-ID: 19737938  |  Reference-DOI: 10.1074/JBC.M109.054973

(-) Compounds

Molecule 1 - KILLERRED
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30-KILLERRED
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ANTHOMEDUSAE SP. DC-2005
    Organism Taxid: 328397

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CRQ2Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID
2SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:97 , HIS A:176 , HOH A:335 , HOH A:344 , ARG B:97 , HIS B:176BINDING SITE FOR RESIDUE SO4 A 238
2AC2SOFTWAREHIS A:152 , LYS A:180 , PRO B:154BINDING SITE FOR RESIDUE SO4 A 239
3AC3SOFTWARELYS A:210 , ILE A:228 , THR A:229 , SER A:230 , ARG B:217BINDING SITE FOR RESIDUE SO4 B 238
4AC4SOFTWAREASP B:209 , LYS B:210 , ARG B:211 , HIS B:213BINDING SITE FOR RESIDUE SO4 B 239

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GB3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:37 -Pro A:38
2Phe A:86 -Pro A:87
3Phe B:37 -Pro B:38
4Phe B:86 -Pro B:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GB3)

(-) Exons   (0, 0)

(no "Exon" information available for 3GB3)

(-) 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:230
 aligned with Q2TCH5_9CNID | Q2TCH5 from UniProtKB/TrEMBL  Length:237

    Alignment length:232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
         Q2TCH5_9CNID     2 EGGPALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIQYGEPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRITSAIG 233
               SCOP domains d3gb3a_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.eeeeeeeeeee..eeeeeeeeeee.....eeeeeeee........hhhhh....--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeeee....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gb3 A   2 EGGPALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIq--EPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRITSAIG 233
                                    11        21        31        41        51        61   |  | 71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
                                                                                          65-CRQ                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:230
 aligned with Q2TCH5_9CNID | Q2TCH5 from UniProtKB/TrEMBL  Length:237

    Alignment length:232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
         Q2TCH5_9CNID     2 EGGPALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIQYGEPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRITSAIG 233
               SCOP domains d3gb3b_ B: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeeeeeeee..eeeeeeeeeee.....eeeeeeee........hhhhh....--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeeee....eeeeeeeeeeee...........eeeeeeeeeee.......eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gb3 B   2 EGGPALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIq--EPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRITSAIG 233
                                    11        21        31        41        51        61   |  | 71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  
                                                                                          65-CRQ
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GB3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GB3)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q2TCH5_9CNID | Q2TCH5)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.

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