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(-) Description

Title :  STRUCTURE OF THE MUTANT V44A OF THE FLUORESCENT PROTEIN KILLERRED
 
Authors :  P. Carpentier, E. De Rosny
Date :  19 Jul 12  (Deposition) - 16 Jan 13  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fluorescent Protein, Photobleaching, Photoconversion, Ros (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. De Rosny, P. Carpentier
Gfp-Like Phototransformation Mechanisms In The Cytotoxic Fluorescent Protein Killerred Unraveled By Structural And Spectroscopic Investigations.
J. Am. Chem. Soc. V. 134 18015 2012
PubMed-ID: 23025285  |  Reference-DOI: 10.1021/JA3073337

(-) Compounds

Molecule 1 - KILLERRED
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET-15B
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ANTHOMEDUSAE SP. DC-2005
    Organism Taxid: 328397
 
Molecule 2 - KILLERRED
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET-15B
    Expression System Vector Type: PLASMID
    Mutation: YES
    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  (6, 22)

Asymmetric/Biological Unit (6, 22)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2CRQ2Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC ACID
3CSO3Mod. Amino AcidS-HYDROXYCYSTEINE
4GOL6Ligand/IonGLYCEROL
5NA2Ligand/IonSODIUM ION
6SO41Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:11 , LYS A:36 , PHE A:37 , ASP A:93 , CL A:1232 , NA A:1236 , NA A:1237 , HOH A:2084 , HOH A:2163BINDING SITE FOR RESIDUE SO4 A1231
02AC2SOFTWARESO4 A:1231BINDING SITE FOR RESIDUE CL A1232
03AC3SOFTWAREARG A:205BINDING SITE FOR RESIDUE CL A1233
04AC4SOFTWAREASP A:32BINDING SITE FOR RESIDUE CL A1234
05AC5SOFTWARELYS A:26BINDING SITE FOR RESIDUE CL A1235
06AC6SOFTWAREASP A:93 , HIS A:107 , SO4 A:1231 , NA A:1237BINDING SITE FOR RESIDUE NA A1236
07AC7SOFTWAREASP A:11 , PHE A:37 , ASP A:93 , HIS A:107 , SO4 A:1231 , NA A:1236BINDING SITE FOR RESIDUE NA A1237
08AC8SOFTWAREHIS B:223 , SER B:224 , HOH B:2088BINDING SITE FOR RESIDUE CL B1233
09AC9SOFTWAREASN B:100BINDING SITE FOR RESIDUE CL B1234
10BC1SOFTWAREARG A:217 , THR B:229 , SER B:230 , HOH B:2089 , HOH B:2093BINDING SITE FOR RESIDUE GOL B1235
11BC2SOFTWAREASN B:155 , SER B:186 , ALA B:188 , PRO B:194 , VAL B:225 , HOH B:2094BINDING SITE FOR RESIDUE GOL B1236
12BC3SOFTWAREGLY A:77 , ILE A:78 , SER A:79 , GLU A:190 , PRO A:192 , GLY A:193 , HOH A:2064 , HOH A:2147BINDING SITE FOR RESIDUE GOL A1239
13BC4SOFTWAREARG A:97 , ASN A:100BINDING SITE FOR RESIDUE GOL A1240
14BC5SOFTWAREGLU A:146 , SER A:186 , THR A:198 , HIS A:223 , HOH A:2164 , HIS B:223BINDING SITE FOR RESIDUE GOL A1241
15BC6SOFTWAREHIS A:152 , LYS A:180 , HOH A:2163BINDING SITE FOR RESIDUE GOL A1242

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B30)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe A:37 -Pro A:38
2Phe A:86 -Pro A:87
3Ile A:228 -Thr A:229
4Phe B:37 -Pro B:38
5Phe B:86 -Pro B:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B30)

(-) Exons   (0, 0)

(no "Exon" information available for 4B30)

(-) 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:227
 aligned with Q2TCH5_9CNID | Q2TCH5 from UniProtKB/TrEMBL  Length:237

    Alignment length:229
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         
         Q2TCH5_9CNID     2 EGGPALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIQYGEPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRITS 230
               SCOP domains d4b30a_ A: 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...........eeeeeeeeeeee......eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b30 A   2 EGGPALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNAHAVCETGKLPMSWKPICHLIq--EPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTcVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVcQREVAYAHSVPRITS 230
                                    11        21        31        41        51        61   |  | 71        81        91       101       111    |  121       131       141       151       161       171       181       191       201       211   |   221         
                                                                                          65-CRQ                                            116-CSO                                                                                            215-CSO           


Chain B from PDB  Type:PROTEIN  Length:229
 aligned with Q2TCH5_9CNID | Q2TCH5 from UniProtKB/TrEMBL  Length:237

    Alignment length:231
                                    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 EGGPALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIQYGEPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRITSAI 232
               SCOP domains d4b30b_ 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...........eeeeeeeeeeee......eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b30 B   2 EGGPALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNAHAVCETGKLPMSWKPICHLIq--EPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTcVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRITSAI 232
                                    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                                            116-CSO
   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 4B30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B30)

(-) 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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  4b30
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 Related Entries

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

UniProtKB/TrEMBL
        Q2TCH5_9CNID | Q2TCH5: 2wiq 2wis 3a8s 3gb3 3gl4 3wck 4zbl 4zfs

(-) Related Entries Specified in the PDB File

2wiq FLUORESCENT PROTEIN KILLERRED IN THE NATIVE STATE
2wis FLUORESCENT PROTEIN KILLERRED IN THE BLEACHED STATE