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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE PLANT PROTEASE DEG1
 
Authors :  T. Clausen
Date :  09 Feb 11  (Deposition) - 04 May 11  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,B,C,D,E,F,G,H,I  (2x)
Keywords :  Protease, Htra, Ph-Sensor, Hydrolase, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kley, B. Schmidt, B. Boyanov, P. C. Stolt-Bergner, R. Kirk, M. Ehrmann, R. R. Knopf, L. Naveh, Z. Adam, T. Clausen
Structural Adaptation Of The Plant Protease Deg1 To Repair Photosystem Ii During Light Exposure.
Nat. Struct. Mol. Biol. V. 18 728 2011
PubMed-ID: 21532594  |  Reference-DOI: 10.1038/NSMB.2055

(-) Compounds

Molecule 1 - PROTEASE DO-LIKE 1, CHLOROPLASTIC
    Chains: A, B, C
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AT3G27925, DEG1, DEGP, DEGP1, K16N12.18
    Organism Common: THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
 
Molecule 2 - PEPTIDE
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 469008
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
 
Molecule 3 - PEPTIDE
    Chains: E, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 469008
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
 
Molecule 4 - PEPTIDE
    Chains: F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 469008
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
 
Molecule 5 - PEPTIDE
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 469008
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHI
Biological Unit 1 (2x): ABCDEFGHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 27)

Asymmetric Unit (1, 27)
No.NameCountTypeFull Name
1UNK27Mod. Amino Acid
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 3QO6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QO6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QO6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QO6)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DEGP1_ARATH326-423
 
 		  3A:326-423
B:326-423
C:326-423
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DEGP1_ARATH326-423
 
 		  6A:326-423
B:326-423
C:326-423

(-) Exons   (0, 0)

(no "Exon" information available for 3QO6)

(-) Sequences/Alignments

Asymmetric 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:326
 aligned with DEGP1_ARATH | O22609 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:326
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430      
          DEGP1_ARATH   111 PKKLQTDELATVRLFQENTPSVVYITNLAVRQDAFTLDVLEVPQGSGSGFVWDKQGHIVTNYHVIRGASDLRVTLADQTTFDAKVVGFDQDKDVAVLRIDAPKNKLRPIPVGVSADLLVGQKVFAIGNPFGLDHTLTTGVISGLRREISSAATGRPIQDVIQTDAAINPGNSGGPLLDSSGTLIGINTAIYSPSGASSGVGFSIPVDTVGGIVDQLVRFGKVTRPILGIKFAPDQSVEQLGVSGVLVLDAPPSGPAGKAGLQSTKRDGYGRLVLGDIITSVNGTKVSNGSDLYRILDQCKVGDEVTVEVLRGDHKEKISVTLEPKP 436
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..eeeeeeeeeee......eeeeeeeeeeeeeee...eeeehhhhhh...eeeee.....eeeeeeeeeehhhheeeee...hhhhh...............eeeeeehhhhh..eeeeeeeeeeeeee........eeeeeee...........eee.....eeeeeeeee.........eeeeehhhhhhhhhhhhhhh....ee..eee.............eeeee....hhhhhhh....ee.....ee...ee.ee.......hhhhhhhhh......eeeeeee....eeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: A:326-423 UniProt: 326-423                                                              ------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qo6 A 111 PKKLQTDELATVRLFQENTPSVVYITNLAVRQDAFTLDVLEVPQGSGSGFVWDKQGHIVTNYHVIRGASDLRVTLADQTTFDAKVVGFDQDKDVAVLRIDAPKNKLRPIPVGVSADLLVGQKVFAIGNPFGLDHTLTTGVISGLRREISSAATGRPIQDVIQTDAAINPGNSGGPLLDSSGTLIGINTAIYSPSGASSGVGFSIPVDTVGGIVDQLVRFGKVTRPILGIKFAPDQSVEQLGVSGVLVLDAPPSGPAGKAGLQSTKRDGYGRLVLGDIITSVNGTKVSNGSDLYRILDQCKVGDEVTVEVLRGDHKEKISVTLEPKP 436
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430      


Chain B from PDB  Type:PROTEIN  Length:328
 aligned with DEGP1_ARATH | O22609 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:328
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430        
          DEGP1_ARATH   111 PKKLQTDELATVRLFQENTPSVVYITNLAVRQDAFTLDVLEVPQGSGSGFVWDKQGHIVTNYHVIRGASDLRVTLADQTTFDAKVVGFDQDKDVAVLRIDAPKNKLRPIPVGVSADLLVGQKVFAIGNPFGLDHTLTTGVISGLRREISSAATGRPIQDVIQTDAAINPGNSGGPLLDSSGTLIGINTAIYSPSGASSGVGFSIPVDTVGGIVDQLVRFGKVTRPILGIKFAPDQSVEQLGVSGVLVLDAPPSGPAGKAGLQSTKRDGYGRLVLGDIITSVNGTKVSNGSDLYRILDQCKVGDEVTVEVLRGDHKEKISVTLEPKPDE 438
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..eeeeeeeeeee......eeeeeeeeeeeeeee...eeeeehhhhh...eeeee.....eeeeeeeeee....eeeeee..hhhhh...............eeeeeehhhhh..eeeeeeeeeeeeeee......eeeeeeee...........eeee....eeeeeeee..........eeeeehhhhhhhhhhhhhhh....ee..eee.....hhhhh...eeeee....hhhhhh.....ee.....ee...eeeee..ee..hhhhhhhhhh......eeeeeee.......eeee.ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: B:326-423 UniProt: 326-423                                                              --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qo6 B 111 PKKLQTDELATVRLFQENTPSVVYITNLAVRQDAFTLDVLEVPQGSGSGFVWDKQGHIVTNYHVIRGASDLRVTLADQTTFDAKVVGFDQDKDVAVLRIDAPKNKLRPIPVGVSADLLVGQKVFAIGNPFGLDHTLTTGVISGLRREISSAATGRPIQDVIQTDAAINPGNSGGPLLDSSGTLIGINTAIYSPSGASSGVGFSIPVDTVGGIVDQLVRFGKVTRPILGIKFAPDQSVEQLGVSGVLVLDAPPSGPAGKAGLQSTKRDGYGRLVLGDIITSVNGTKVSNGSDLYRILDQCKVGDEVTVEVLRGDHKEKISVTLEPKPDE 438
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430        


Chain C from PDB  Type:PROTEIN  Length:328
 aligned with DEGP1_ARATH | O22609 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:328
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428        
          DEGP1_ARATH   109 STPKKLQTDELATVRLFQENTPSVVYITNLAVRQDAFTLDVLEVPQGSGSGFVWDKQGHIVTNYHVIRGASDLRVTLADQTTFDAKVVGFDQDKDVAVLRIDAPKNKLRPIPVGVSADLLVGQKVFAIGNPFGLDHTLTTGVISGLRREISSAATGRPIQDVIQTDAAINPGNSGGPLLDSSGTLIGINTAIYSPSGASSGVGFSIPVDTVGGIVDQLVRFGKVTRPILGIKFAPDQSVEQLGVSGVLVLDAPPSGPAGKAGLQSTKRDGYGRLVLGDIITSVNGTKVSNGSDLYRILDQCKVGDEVTVEVLRGDHKEKISVTLEPKP 436
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------Trypsin_2-3qo6C04 C:157-296                                                                                                                 --------------------------------------PDZ_2-3qo6C01 C:335-432                                                                           ---- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------Trypsin_2-3qo6C05 C:157-296                                                                                                                 --------------------------------------PDZ_2-3qo6C02 C:335-432                                                                           ---- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------Trypsin_2-3qo6C06 C:157-296                                                                                                                 --------------------------------------PDZ_2-3qo6C03 C:335-432                                                                           ---- Pfam domains (3)
         Sec.struct. author ......hhhhhhhhhhhhhhh..eeeeeeeeeee......eeeeeeeeeeeee.....eeeehhhhhh...eeeee.....eeeeeeeeee....eeeeee......................eeeeeehhhhh..eeeeeeeeeeeeee........eeeeeee...........eee.....eeeeeeee..........eeeeehhhhhhhhhhhhhhh....ee..eee.hhhhh.......eeeee....hhhhhh.....ee.....ee...eeee.......hhhhhhhhhhh.....eeeeeeee..eeeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: C:326-423 UniProt: 326-423                                                              ------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qo6 C 109 STPKKLQTDELATVRLFQENTPSVVYITNLAVRQDAFTLDVLEVPQGSGSGFVWDKQGHIVTNYHVIRGASDLRVTLADQTTFDAKVVGFDQDKDVAVLRIDAPKNKLRPIPVGVSADLLVGQKVFAIGNPFGLDHTLTTGVISGLRREISSAATGRPIQDVIQTDAAINPGNSGGPLLDSSGTLIGINTAIYSPSGASSGVGFSIPVDTVGGIVDQLVRFGKVTRPILGIKFAPDQSVEQLGVSGVLVLDAPPSGPAGKAGLQSTKRDGYGRLVLGDIITSVNGTKVSNGSDLYRILDQCKVGDEVTVEVLRGDHKEKISVTLEPKP 436
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428        


Chain D from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ...eee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3qo6 D   0 xxxxxxx   6
                            |||||||
                            0-UNK||
                             1-UNK|
                              2-UNK
                               3-UNK
                                4-UNK
                                 5-UNK
                                  6-UNK


Chain E from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3qo6 E   1 xxxx   4
                            ||||
                            ||||
                            1-UNK
                             2-UNK
                              3-UNK
                               4-UNK


Chain F from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3qo6 F   1 xxxxx   5
                            |||||
                            |||||
                            1-UNK
                             2-UNK
                              3-UNK
                               4-UNK
                                5-UNK


Chain G from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author .ee Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3qo6 G   1 xxx   3
                            |||
                            |||
                            1-UNK
                             2-UNK
                              3-UNK


Chain H from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .eee Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3qo6 H   1 xxxx   4
                            ||||
                            ||||
                            1-UNK
                             2-UNK
                              3-UNK
                               4-UNK


Chain I from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .eee Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3qo6 I   1 xxxx   4
                            ||||
                            ||||
                            1-UNK
                             2-UNK
                              3-UNK
                               4-UNK
   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  (0, 0)

(no "SCOP Domain" information available for 3QO6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QO6)

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: PDZ-like (184)
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DEGP1_ARATH | O22609)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0010206    photosystem II repair    Proteolysis of the damaged D1 protein and re-assembly of a new D1 subunit in the photosystem II following photoinhibition.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0009735    response to cytokinin    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 cytokinin stimulus.
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:0009534    chloroplast thylakoid    Sac-like membranous structures (cisternae) in a chloroplast combined into stacks (grana) and present singly in the stroma (stroma thylakoids or frets) as interconnections between grana. An example of this component is found in Arabidopsis thaliana.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
    GO:0031977    thylakoid lumen    The volume enclosed by a thylakoid membrane.

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 Related Entries

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