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(-) Description

Title :  X-RAY STRUCTURE OF A LYSINE DECARBOXYLASE-LIKE PROTEIN FROM ARABIDOPSIS THALIANA GENE AT5G11950
 
Authors :  G. E. Wesenberg, G. N. Phillips Jr. , E. Bitto, C. A. Bingman, S. T. M. Allard, Center For Eukaryotic Structural Genomics (Cesg)
Date :  23 Dec 04  (Deposition) - 11 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, At5G11950, Lysine Decarboxylase-Like Protein, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. B. Jeon, S. T. M. Allard, C. A. Bingman, E. Bitto, B. W. Han, G. E. Wesenberg, G. N. Phillips Jr.
X-Ray Crystal Structures Of The Conserved Hypothetical Proteins From Arabidopsis Thaliana Gene Loci At5G11950 And At2G37210.
Proteins V. 65 1051 2006
PubMed-ID: 17048257  |  Reference-DOI: 10.1002/PROT.21166
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AT5G11950
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP-13
    Expression System Strain: B834(DE3) P(LACI+RARE)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT5G11950
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric/Biological Unit (3, 21)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE16Mod. Amino AcidSELENOMETHIONINE
3NO31Ligand/IonNITRATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:84 , HOH A:825 , VAL B:89 , ARG B:90 , HOH B:813BINDING SITE FOR RESIDUE NO3 A 600
2AC2SOFTWAREARG B:168 , VAL B:171 , SER B:173 , HOH B:734BINDING SITE FOR RESIDUE EDO B 700
3AC3SOFTWARETYR A:62 , THR A:85 , GLY A:87 , HOH A:742 , HOH A:757 , HOH A:782 , GLY B:87 , ASP B:88 , HOH B:815BINDING SITE FOR RESIDUE EDO A 701
4AC4SOFTWAREGLY A:161 , HIS B:19 , SER B:20 , GLY B:21BINDING SITE FOR RESIDUE EDO B 702
5AC5SOFTWAREGLY A:17 , SER A:18 , HIS A:19 , GLY A:114 , GLY A:115 , THR A:118 , HOH A:709 , HOH A:717 , PHE B:162BINDING SITE FOR RESIDUE EDO A 703

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YDH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YDH)

(-) 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:184
 aligned with LOG8_ARATH | Q84MC2 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:184
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
           LOG8_ARATH     5 QRSRFRKICVFCGSHSGHREVFSDAAIELGNELVKRKIDLVYGGGSVGLMGLISRRVYEGGLHVLGIIPKALMPIEISGETVGDVRVVADMHERKAAMAQEAEAFIALPGGYGTMEELLEMITWSQLGIHKKTVGLLNVDGYYNNLLALFDTGVEEGFIKPGARNIVVSAPTAKELMEKMEEYT 188
               SCOP domains d1ydha_ A: Hypothetical protein At5g11950                                                                                                                                                SCOP domains
               CATH domains 1ydhA00 A:5-188  [code=3.40.50.450, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.......hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh...eeeeee..hhhhhh......eeeee.hhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh...hhhhhh.eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydh A   5 QRSRFRKICVFCGSHSGHREVFSDAAIELGNELVKRKIDLVYGGGSVGLmGLISRRVYEGGLHVLGIIPKALmPIEISGETVGDVRVVADmHERKAAmAQEAEAFIALPGGYGTmEELLEmITWSQLGIHKKTVGLLNVDGYYNNLLALFDTGVEEGFIKPGARNIVVSAPTAKELmEKmEEYT 188
                                    14        24        34        44        54        64        74  |     84        94|      104       114    |  124|      134       144       154       164       174      |184    
                                                                            54-MSE                 77-MSE            95-MSE  |              119-MSE |                                                     181-MSE   
                                                                                                                           102-MSE                125-MSE                                                    184-MSE


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with LOG8_ARATH | Q84MC2 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:181
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 
           LOG8_ARATH     8 RFRKICVFCGSHSGHREVFSDAAIELGNELVKRKIDLVYGGGSVGLMGLISRRVYEGGLHVLGIIPKALMPIEISGETVGDVRVVADMHERKAAMAQEAEAFIALPGGYGTMEELLEMITWSQLGIHKKTVGLLNVDGYYNNLLALFDTGVEEGFIKPGARNIVVSAPTAKELMEKMEEYT 188
               SCOP domains d1ydhb_ B: Hypothetical protein At5g11950                                                                                                                                             SCOP domains
               CATH domains 1ydhB00 B:8-188  [code=3.40.50.450, no name defined]                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee........hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh...eeeeee..hhhhhh......eeeee.hhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh...hhhhhh.eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydh B   8 RFRKICVFCGSHSGHREVFSDAAIELGNELVKRKIDLVYGGGSVGLmGLISRRVYEGGLHVLGIIPKALmPIEISGETVGDVRVVADmHERKAAmAQEAEAFIALPGGYGTmEELLEmITWSQLGIHKKTVGLLNVDGYYNNLLALFDTGVEEGFIKPGARNIVVSAPTAKELmEKmEEYT 188
                                    17        27        37        47      | 57        67        77        87       |97    |  107       117 |     127       137       147       157       167       177   |  |187 
                                                                         54-MSE                 77-MSE            95-MSE  |              119-MSE |                                                     181-MSE   
                                                                                                                        102-MSE                125-MSE                                                    184-MSE
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YDH)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LOG8_ARATH | Q84MC2)
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:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0009691    cytokinin biosynthetic process    The chemical reactions and pathways resulting in the formation of cytokinins, a class of adenine-derived compounds that can function in plants as growth regulators.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LOG8_ARATH | Q84MC2: 2q4d

(-) Related Entries Specified in the PDB File

2a33 60 PERCENT SEQUENCE IDENTITY, SAME FOLD RELATED ID: GO.19912 RELATED DB: TARGETDB