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(-) Description

Title :  CRYSTAL STRUCTURE OF CRYPTOCHROME 3 FROM ARABIDOPSIS THALIANA
 
Authors :  Y. Huang, J. Deisenhofer
Date :  29 Sep 06  (Deposition) - 28 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  X
Keywords :  Photolyase; Cryptochrome, Lyase, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Huang, R. Baxter, B. S. Smith, C. L. Partch, C. L. Colbert, J. Deisenhofer
Crystal Structure Of Cryptochrome 3 From Arabidopsis Thaliana And Its Implications For Photolyase Activity
Proc. Natl. Acad. Sci. Usa V. 103 17701 2006
PubMed-ID: 17101984  |  Reference-DOI: 10.1073/PNAS.0608554103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CRYPTOCHROME DASH, CHLOROPLAST/MITOCHONDRIAL
    ChainsX
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCRYD
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymCRYPTOCHROME 3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MHF1Ligand/Ion5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR X:272 , SER X:285 , THR X:286 , LYS X:287 , PHE X:288 , SER X:289 , LEU X:292 , GLU X:325 , ARG X:329 , PHE X:332 , PHE X:388 , ASN X:391 , ARG X:394 , GLN X:395 , ASP X:422 , TYR X:423 , ASP X:424 , SER X:427 , ASN X:428 , ASN X:431 , TRP X:432 , HOH X:530 , HOH X:533 , HOH X:572 , HOH X:609 , HOH X:623BINDING SITE FOR RESIDUE FAD X 526
2AC2SOFTWAREHIS X:84 , LYS X:90 , CYS X:147 , SER X:148 , GLU X:149 , GLU X:150 , PHE X:188 , ASP X:189 , ASP X:192 , LYS X:338 , ASN X:341 , PHE X:344 , HIS X:345 , GLU X:417 , TYR X:423 , PRO X:425 , TYR X:429 , HOH X:541 , HOH X:579BINDING SITE FOR RESIDUE MHF X 527

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val X:8 -Pro X:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHR_CRY_ALPHA_BETAPS51645 Photolyase/cryptochrome alpha/beta domain profile.CRYD_ARATH84-221  1X:41-177

(-) Exons   (0, 0)

(no "Exon" information available for 2IJG)

(-) 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 X from PDB  Type:PROTEIN  Length:492
 aligned with CRYD_ARATH | Q84KJ5 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:497
                                    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       463       473       483       493       503       513       523       533       
           CRYD_ARATH    44 MNDHIHRVPALTEEEIDSVAIKTFERYALPSSSSVKRKGKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGLKRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPREDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPLKH 540
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....hhhhhhhhhhhhhhhh....----......eeeee.........hhhhhhhhhh..eeeeeeeehhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh-...eeeee......hhhhh..hhhhh..hhhhhhhhhhhhh..........................hhhhh........ee....hhhhhhhhhhhhhh..hhhhhhhhhh...........hhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhh...hhhhhhhhhh..hhhhhhhhhhhh..hhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------PHR_CRY_ALPHA_BETA  PDB: X:41-177 UniProt: 84-221                                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ijg X   1 MNDHIHRVPALTEEEIDSVAIKTFERYALPS----KRKGKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGLKRV-NSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPREDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPLKH 496
                                    10        20        30|    |  40        50        60        70        80        90       100       110       120       130       140       150       160   | | 169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       
                                                         31   36                                                                                                                             164 |                                                                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                               165                                                                                                                                                                                                                                                                                                                                           

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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  (0, 0)

(no "SCOP Domain" information available for 2IJG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IJG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (CRYD_ARATH | Q84KJ5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003913    DNA photolyase activity    Catalysis of the repair of a photoproduct resulting from ultraviolet irradiation of two adjacent pyrimidine residues in DNA.
    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:0009881    photoreceptor activity    The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
    GO:0050896    response to stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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 Related Entries

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        CRYD_ARATH | Q84KJ52j4d 2vtb

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