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(-) Description

Title :  X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G06450
 
Authors :  G. E. Wesenberg, D. W. Smith, G. N. Phillips Jr. , K. A. Johnson, C. A. Bin Center For Eukaryotic Structural Genomics (Cesg)
Date :  12 Apr 04  (Deposition) - 27 Apr 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Protein, Homohexamer, Arabidopsis Thaliana, At5G06450, Structural Genomics, Protein Structure Initiative, Center For Eukaryotic Structural Genomics, Cesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Center For Eukaryotic Structural Genomics
X-Ray Structure Of Gene Product From Arabidopsis Thaliana At5G06450
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AT5G06450
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VK0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VK0)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Lys B:91 -Pro B:92
2Lys C:91 -Pro C:92
3Lys D:91 -Pro D:92
4Lys E:91 -Pro E:92
5Lys F:91 -Pro F:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VK0)

(-) Exons   (0, 0)

(no "Exon" information available for 1VK0)

(-) 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:200
 aligned with Y5645_ARATH | Q9FNG3 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
          Y5645_ARATH     1 MASFDGPKFKMTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
               SCOP domains d1vk0a_ A: Hypothetical protein AT5G06450                                                                                                                                                                      SCOP domains
               CATH domains 1vk0A00 A:1-206  [code=3.30.420.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eeeeeeee......hhhhhhhhhhhhhhhh..eeeeeeeee...------hhhhhheeeeeeee...eeeeee.....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk0 A   1 SASFDGPKFKmTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGF------TKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
                                    10|       20        30        40        50        |-     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200      
                                     11-MSE                                          59     66                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:200
 aligned with Y5645_ARATH | Q9FNG3 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
          Y5645_ARATH     1 MASFDGPKFKMTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
               SCOP domains d1vk0b_ B: Hypothetical protein AT5G06450                                                                                                                                                                      SCOP domains
               CATH domains 1vk0B00 B:1-206  [code=3.30.420.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eeeeeeee......hhhhhhhhhhhhhhhh..eeeeeeeee...------......eeeeeeee...eeeeee.....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk0 B   1 SASFDGPKFKmTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGF------TKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
                                    10|       20        30        40        50        |-     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200      
                                     11-MSE                                          59     66                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:200
 aligned with Y5645_ARATH | Q9FNG3 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
          Y5645_ARATH     1 MASFDGPKFKMTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
               SCOP domains d1vk0c_ C: Hypothetical protein AT5G06450                                                                                                                                                                      SCOP domains
               CATH domains 1vk0C00 C:1-206  [code=3.30.420.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eeeeeeee......hhhhhhhhhhhhhhhh..eeeeeeeee...------......eeeeeeee...eeeeee.....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk0 C   1 SASFDGPKFKmTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGF------TKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
                                    10|       20        30        40        50        |-     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200      
                                     11-MSE                                          59     66                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:200
 aligned with Y5645_ARATH | Q9FNG3 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
          Y5645_ARATH     1 MASFDGPKFKMTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
               SCOP domains d1vk0d_ D: Hypothetical protein AT5G06450                                                                                                                                                                      SCOP domains
               CATH domains 1vk0D00 D:1-206  [code=3.30.420.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eeeeeeee......hhhhhhhhhhhhhhhh..eeeeeeeee...------......eeeeeeee...eeeeee.....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk0 D   1 SASFDGPKFKmTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGF------TKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
                                    10|       20        30        40        50        |-     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200      
                                     11-MSE                                          59     66                                                                                                                                            


Chain E from PDB  Type:PROTEIN  Length:200
 aligned with Y5645_ARATH | Q9FNG3 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
          Y5645_ARATH     1 MASFDGPKFKMTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
               SCOP domains d1vk0e_ E: Hypothetical protein AT5G06450                                                                                                                                                                      SCOP domains
               CATH domains 1vk0E00 E:1-206  [code=3.30.420.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eeeeeeee......hhhhhhhhhhhhhhhh..eeeeeeeee...------hhhhhheeeeeeee...eeeeee.....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk0 E   1 SASFDGPKFKmTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGF------TKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
                                    10|       20        30        40        50        |-     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200      
                                     11-MSE                                          59     66                                                                                                                                            


Chain F from PDB  Type:PROTEIN  Length:200
 aligned with Y5645_ARATH | Q9FNG3 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
          Y5645_ARATH     1 MASFDGPKFKMTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
               SCOP domains d1vk0f_ F: Hypothetical protein AT5G06450                                                                                                                                                                      SCOP domains
               CATH domains 1vk0F00 F:1-206  [code=3.30.420.10, no name defined]                                                                                                                                                           CATH domains
           Pfam domains (1) --------------------------------------DNA_pol_A_exo1-1vk0F0      1 F:39-206                                                                                                                                    Pfam domains (1)
           Pfam domains (2) --------------------------------------DNA_pol_A_exo1-1vk0F0      2 F:39-206                                                                                                                                    Pfam domains (2)
           Pfam domains (3) --------------------------------------DNA_pol_A_exo1-1vk0F0      3 F:39-206                                                                                                                                    Pfam domains (3)
           Pfam domains (4) --------------------------------------DNA_pol_A_exo1-1vk0F0      4 F:39-206                                                                                                                                    Pfam domains (4)
           Pfam domains (5) --------------------------------------DNA_pol_A_exo1-1vk0F0      5 F:39-206                                                                                                                                    Pfam domains (5)
           Pfam domains (6) --------------------------------------DNA_pol_A_exo1-1vk0F0      6 F:39-206                                                                                                                                    Pfam domains (6)
         Sec.struct. author .......eee.....eeeeeeee......hhhhhhhhhhhhhhhh..eeeeeeeee...------hhhhhheeeeeeee...eeeeee.....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk0 F   1 SASFDGPKFKmTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGF------TKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
                                    10|       20        30        40        50        |-     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200      
                                     11-MSE                                          59     66
   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  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Y5645_ARATH | Q9FNG3)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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    Lys B:91 - Pro B:92   [ RasMol ]  
    Lys C:91 - Pro C:92   [ RasMol ]  
    Lys D:91 - Pro D:92   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        Y5645_ARATH | Q9FNG3: 2q3s

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VK0)