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(-) Description

Title :  CRYSTAL STRUCTURE OF L-ASPARTATE-ALPHA-DECARBOXYLASE
 
Authors :  O. Nakajima, Riken Structural Genomics/Proteomics Initiative (
Date :  04 Mar 04  (Deposition) - 28 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (4x)
Keywords :  Tetramer, Pyruvoyl Group, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Goto, R. Omi, O. Nakajima, I. Miyahara, K. Hirotsu
Crystal Structure Of L-Aspartate-Alpha-Decarboxylase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-ASPARTATE-ALPHA-DECARBOXYLASE LIGHT CHAIN
    Chains: A
    EC Number: 4.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HB8
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
 
Molecule 2 - L-ASPARTATE-ALPHA-DECARBOXYLASE HEAVY CHAIN
    Chains: B
    EC Number: 4.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HB8
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (4x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PYR1Mod. Amino AcidPYRUVIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PYR2Mod. Amino AcidPYRUVIC ACID
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1PYR4Mod. Amino AcidPYRUVIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1VC3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VC3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VC3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VC3)

(-) Exons   (0, 0)

(no "Exon" information available for 1VC3)

(-) 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:24
 aligned with PAND_THET8 | Q5SKN7 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:24
                                    10        20    
           PAND_THET8     1 MKRVMFHAKIHRATVTQADLHYVG  24
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                 1vc3 A   1 MKRVMFHAKIHRATVTQADLHYVG  24
                                    10        20    


Chain B from PDB  Type:PROTEIN  Length:96
 aligned with PAND_THET8 | Q5SKN7 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:96
                                    34        44        54        64        74        84        94       104       114      
           PAND_THET8    25 SVTVDQDLLDAAGILPFEQVDIYDITNGARLTTYALPGERGSGVIGINGAAAHLVKPGDLVILVAYGVFDEEEARNLKPTVVLVDERNRILEVRKG 120
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -1vc3B00 B:26-120  [code=2.40.40.20, no name defined]                                            CATH domains
           Pfam domains (1) -Asp_decarbox-1vc3B01 B:26-116                                                              ---- Pfam domains (1)
           Pfam domains (2) -Asp_decarbox-1vc3B02 B:26-116                                                              ---- Pfam domains (2)
         Sec.struct. author ..eeehhhhhhhh.....eeeeee.....eeeee.eee......eeee.hhhhh.....eeeeeeeeeehhhhhh....eeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1vc3 B  25 xVTVDQDLLDAAGILPFEQVDIYDITNGARLTTYALPGERGSGVIGINGAAAHLVKPGDLVILVAYGVFDEEEARNLKPTVVLVDERNRILEVRKG 120
                            |       34        44        54        64        74        84        94       104       114      
                           25-PYR
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 1VC3)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: AcetylDC-like (37)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PAND_THET8 | Q5SKN7)
molecular function
    GO:0004068    aspartate 1-decarboxylase activity    Catalysis of the reaction: L-aspartate = beta-alanine + CO2.
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006523    alanine biosynthetic process    The chemical reactions and pathways resulting in the formation of alanine, 2-aminopropanoic acid.
    GO:0015940    pantothenate biosynthetic process    The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        PAND_THET8 | Q5SKN7: 2eeo

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