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(-) Description

Title :  PROCESSED ASPARTATE DECARBOXYLASE MUTANT WITH SER25 MUTATED TO CYS
 
Authors :  F. Schmitzberger, M. L. Kilkenny, C. M. C. Lobley, M. E. Webb, M. Vinkovi D. Matak-Vinkovic, M. Witty, D. Y. Chirgadze, A. G. Smith, C. Abell, T. L. Blundell
Date :  09 Jul 03  (Deposition) - 18 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Auto-Processing, Aspartate Decarboxylase, Pyruvoyl, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Schmitzberger, M. L. Kilkenny, C. M. C. Lobley, M. E. Webb, M. Vinkovic, D. Matak-Vinkovic, M. Witty, D. Y. Chirgadze, A. G. Smith C. Abell, T. L. Blundell
Structural Constraints On Protein Self-Processing In L-Aspartate-Alpha-Decarboxylase
Embo J. V. 22 6193 2003
PubMed-ID: 14633979  |  Reference-DOI: 10.1093/EMBOJ/CDG575
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ASPARTATE 1-DECARBOXYLASE BETA CHAIN
    Chains: A, C
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETA
    Expression System Strain: C41 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PAND
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ASPARTATE ALPHA-DECARBOXYLASE
 
Molecule 2 - ASPARTATE 1-DECARBOXYLASE ALFA CHAIN
    Chains: B, D
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETA
    Expression System Strain: C41 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PAND
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ASPARTATE ALPHA-DECARBOXYLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP B:47 , ARG B:54 , ILE B:86 , CYS D:25 , THR D:57 , ASN D:72 , GLY D:73 , ALA D:74 , ALA D:75 , HOH D:233BINDING SITE FOR RESIDUE SO4 D 201
2AC2SOFTWARECYS B:25 , THR B:57 , ASN B:72 , ALA B:74 , ALA B:75 , TRP D:47 , ARG D:54 , ILE D:86BINDING SITE FOR RESIDUE SO4 B 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PYU)

(-) 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:28
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:28
                                1                       
                                |    6        16        
           PAND_ECOLI     - ----MIRTMLQGKLHRVKVTHADLHYEG  24
               SCOP domains d1pyu.1 A:,B:                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
                 1pyu A  -3 PRGSMIRTMLQGKLHRVKVTHADLHYEG  24
                                     6        16        


Chain B from PDB  Type:PROTEIN  Length:92
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:92
                                    34        44        54        64        74        84        94       104       114  
           PAND_ECOLI    25 SCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKR 116
               SCOP domains d1pyu.1 A:,B: Pyruvoyl dependent aspartate decarboxylase, ADC                                SCOP domains
               CATH domains 1pyuB00 B:25-116  [code=2.40.40.20, no name defined]                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhh.....eeeeee.....eeeeeeeee......eeee.hhhhh.....eeeeeeeeeeehhhhhhh..eeeeee...ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 1pyu B  25 CCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKR 116
                                    34        44        54        64        74        84        94       104       114  


Chain C from PDB  Type:PROTEIN  Length:24
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:24
                                    10        20    
           PAND_ECOLI     1 MIRTMLQGKLHRVKVTHADLHYEG  24
               SCOP domains d1pyu.2 C:,D:            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
                 1pyu C   1 MIRTMLQGKLHRVKVTHADLHYEG  24
                                    10        20    


Chain D from PDB  Type:PROTEIN  Length:91
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:91
                                    34        44        54        64        74        84        94       104       114 
           PAND_ECOLI    25 SCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMK 115
               SCOP domains d1pyu.2 C:,D: Pyruvoyl dependent aspartate decarboxylase, ADC                               SCOP domains
               CATH domains 1pyuD00 D:25-115  [code=2.40.40.20, no name defined]                                        CATH domains
           Pfam domains (1) -Asp_decarbox-1pyuD01 D:26-115                                                              Pfam domains (1)
           Pfam domains (2) -Asp_decarbox-1pyuD02 D:26-115                                                              Pfam domains (2)
           Pfam domains (3) -Asp_decarbox-1pyuD03 D:26-115                                                              Pfam domains (3)
           Pfam domains (4) -Asp_decarbox-1pyuD04 D:26-115                                                              Pfam domains (4)
         Sec.struct. author .eeeehhhhhhhh.....eeeeee.....eeeeeeeee......eeee.hhhhh.....eeeeeeeeeeehhhhh....eeeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1pyu D  25 CCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMK 115
                                    34        44        54        64        74        84        94       104       114
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PAND_ECOLI | P0A790)
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.
    GO:0016540    protein autoprocessing    Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PAND_ECOLI | P0A790: 1aw8 1ppy 1pqe 1pqf 1pqh 1pt0 1pt1 1pyq 3tm7 4aok 4aon 4azd 4cry 4crz 4cs0 4d7z

(-) Related Entries Specified in the PDB File

1aw8 PYRUVOYL-DEPENDENT ASPARTATE DECARBOXYLASE
1ppy
1pqe
1pqf
1pqh
1pt0
1pt1
1pyq