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(-) Description

Title :  X-RAY STRUCTURE OF A LYSINE DECARBOXYLASE-LIKE PROTEIN FROM ARABIDOPSIS THALIANA GENE AT2G37210
 
Authors :  G. E. Wesenberg, G. N. Phillips Jr. , J. G. Mccoy, E. Bitto, C. A. Bingman, S. T. M. Allard, Center For Eukaryotic Structural Genomics (Cesg)
Date :  23 Jun 05  (Deposition) - 19 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, At2G37210, 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 - HYPOTHETICAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP-13
    Expression System Strain: B834 P(RARE2)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT2G37210
    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, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:700 , SER B:22 , GLY B:118 , GLY B:119 , TYR B:120 , GLY B:121 , THR B:122 , HOH B:719 , HOH B:737 , HOH B:751BINDING SITE FOR RESIDUE SO4 B 500
2AC2SOFTWARESER A:22 , GLY A:119 , TYR A:120 , GLY A:121 , THR A:122 , HOH A:606 , HOH A:617 , HOH A:635 , HOH B:785BINDING SITE FOR RESIDUE SO4 A 600
3AC3SOFTWAREASP B:139 , HOH B:764 , HOH B:816 , HOH B:817 , HOH B:818BINDING SITE FOR RESIDUE MG B 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A33)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A33)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A33)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A33)

(-) Exons   (0, 0)

(no "Exon" information available for 2A33)

(-) 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:175
 aligned with LOG3_ARATH | Q8L8B8 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:183
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187   
           LOG3_ARATH     8 MQKSKFRRICVFCGSSQGKKSSYQDAAVDLGNELVSRNIDLVYGGGSIGLMGLVSQAVHDGGRHVIGIIPKTLMPRELTGETVGEVRAVADMHQRKAEMAKHSDAFIALPGGYGTLEELLEVITWAQLGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGFISPTAREIIVSAPTAKELVKKLEE 190
               SCOP domains d2a33a1 A:8-190 Hypothetical protein At2g37210/T2N18.3                                                                                                                                  SCOP domains
               CATH domains -2a33A00 A:9-190  [code=3.40.50.450, no name defined]                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.......hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh...eeeeee....--------..eeeee.hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhh...hhhhhh.eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a33 A   8 mQKSKFRRICVFCGSSQGKKSSYQDAAVDLGNELVSRNIDLVYGGGSIGLmGLVSQAVHDGGRHVIGIIPKTLm--------VGEVRAVADmHQRKAEmAKHSDAFIALPGGYGTLEELLEVITWAQLGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGFISPTAREIIVSAPTAKELVKKLEE 190
                            |       17        27        37        47        57|       67        77   |     -  |     97 |     107       117       127       137       147       157       167       177       187   
                            |                                                58-MSE                 81-MSE   90       99-MSE  |                                                                                    
                            8-MSE                                                                                           106-MSE                                                                                


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with LOG3_ARATH | Q8L8B8 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:181
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 
           LOG3_ARATH    10 KSKFRRICVFCGSSQGKKSSYQDAAVDLGNELVSRNIDLVYGGGSIGLMGLVSQAVHDGGRHVIGIIPKTLMPRELTGETVGEVRAVADMHQRKAEMAKHSDAFIALPGGYGTLEELLEVITWAQLGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGFISPTAREIIVSAPTAKELVKKLEE 190
               SCOP domains d2a33b_ B: Hypothetical protein At2g37210/T2N18.3                                                                                                                                     SCOP domains
               CATH domains 2a33B00 B:10-190  [code=3.40.50.450, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.......hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh...eeeeee.--------.....eeeee.hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhh...hhhhhh.eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a33 B  10 KSKFRRICVFCGSSQGKKSSYQDAAVDLGNELVSRNIDLVYGGGSIGLmGLVSQAVHDGGRHVIGIIPK--------GETVGEVRAVADmHQRKAEmAKHSDAFIALPGGYGTLEELLEVITWAQLGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGFISPTAREIIVSAPTAKELVKKLEE 190
                                    19        29        39        49        59        69        |-       |89        99      |109       119       129       139       149       159       169       179       189 
                                                                           58-MSE              78       87          99-MSE  |                                                                                    
                                                                                                                          106-MSE
   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) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A33)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LOG3_ARATH | Q8L8B8)
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.
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: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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  2a33
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 Related Entries

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

UniProtKB/Swiss-Prot
        LOG3_ARATH | Q8L8B8: 2q4o

(-) Related Entries Specified in the PDB File

1ydh 60 PERCENT SEQUENCE IDENTITY, SAME FOLD RELATED ID: GO.9733 RELATED DB: TARGETDB