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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ASPARTATE ALPHA-DECARBOXYLASE FROM CAMPYLOBACTER JEJUNI SUBSP. JEJUNI NCTC 11168
 
Authors :  K. Tan, M. Gu, S. Peterson, W. F. Anderson, A. Joachimiak, Center For S Genomics Of Infectious Diseases (Csgid)
Date :  15 Nov 10  (Deposition) - 08 Dec 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Double-Psi Beta-Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, M. Gu, S. Peterson, W. F. Anderson, A. Joachimiak
The Crystal Structure Of Aspartate Alpha-Decarboxylase From Campylobacter Jejuni Subsp. Jejuni Nctc 11168
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ASPARTATE 1-DECARBOXYLASE
    Chains: A
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-24
    Gene: CJ0296C, PAND
    Organism Scientific: CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168
    Synonym: ASPARTATE ALPHA-DECARBOXYLASE, ASPARTATE 1-DECARBOXYLASE BETA CHAIN, ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN
 
Molecule 2 - ASPARTATE 1-DECARBOXYLASE
    Chains: B
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 25-126
    Gene: CJ0296C, PAND
    Organism Scientific: CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168
    Synonym: ASPARTATE ALPHA-DECARBOXYLASE, ASPARTATE 1-DECARBOXYLASE BETA CHAIN, ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PYR1Mod. Amino AcidPYRUVIC ACID
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
3PYR4Mod. Amino AcidPYRUVIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPYR B:25 , VAL B:47 , ARG B:54 , THR B:57 , ASN B:71 , GLY B:72 , ALA B:73 , ALA B:74 , ILE B:85BINDING SITE FOR RESIDUE ACT B 1
2AC2SOFTWARETHR A:16 , GLU B:65 , GLY B:66 , GLU B:109BINDING SITE FOR RESIDUE PEG B 127

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PLX)

(-) Exons   (0, 0)

(no "Exon" information available for 3PLX)

(-) 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:25
 aligned with PAND_CAMJE | Q9PIK3 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:25
                             1                       
                             |       9        19     
           PAND_CAMJE     - -MNITLLKSKIHRASVTEARLDYIG  24
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee..eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 3plx A   0 AMNITLLKSKIHRASVTEARLDYIG  24
                                     9        19     


Chain B from PDB  Type:PROTEIN  Length:101
 aligned with PAND_CAMJE | Q9PIK3 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:101
                                    34        44        54        64        74        84        94       104       114       124 
           PAND_CAMJE    25 SISIDEKLLQASGILEYEKVQVVNVNNGARFETYTIATQEEGVVCLNGAAARLAEVGDKVIIMSYADFNEEEAKTFKPKVVFVDENNTATKITNYEKHGAI 125
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Asp_decarbox-3plxB01 B:26-115                                                             ---------- Pfam domains (1)
           Pfam domains (2) -Asp_decarbox-3plxB02 B:26-115                                                             ---------- Pfam domains (2)
         Sec.struct. author ..eeehhhhhhhh.....eeeeee.....eeeee.eee.....eeee.hhhhhh....eeeeeeeeeeehhhhhhh..eeeee.....eeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3plx B  25 xISIDEKLLQASGILEYEKVQVVNVNNGARFETYTIATQEEGVVCLNGAAARLAEVGDKVIIMSYADFNEEEAKTFKPKVVFVDENNTATKITNYEKHGAI 125
                            |       34        44        54        64        74        84        94       104       114       124 
                           25-PYR
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PAND_CAMJE | Q9PIK3)
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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