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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPARTATE DECARBOXYLASE, ISOASPARGINE COMPLEX
 
Authors :  B. I. Lee, A. -R. Kwon, B. W. Han, S. W. Suh
Date :  01 Jul 03  (Deposition) - 13 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Biol. Unit 2:  A,B  (8x)
Keywords :  Double-Psi Beta Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. I. Lee, S. W. Suh
Crystal Structure Of The Schiff Base Intermediate Prior To Decarboxylation In The Catalytic Cycle Of Aspartate Alpha-Decarboxylase
J. Mol. Biol. V. 340 1 2004
PubMed-ID: 15184017  |  Reference-DOI: 10.1016/J.JMB.2004.04.049

(-) Compounds

Molecule 1 - ASPARTATE 1-DECARBOXYLASE BETA CHAIN
    Chains: B
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PAND
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
 
Molecule 2 - ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN
    Chains: A
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PAND
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB
Biological Unit 2 (8x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NSN1Ligand/IonN~2~-(2-AMINO-1-METHYL-2-OXOETHYLIDENE)ASPARAGINATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NSN4Ligand/IonN~2~-(2-AMINO-1-METHYL-2-OXOETHYLIDENE)ASPARAGINATE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1NSN8Ligand/IonN~2~-(2-AMINO-1-METHYL-2-OXOETHYLIDENE)ASPARAGINATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:26 , ARG A:54 , THR A:57 , TYR A:58 , ILE A:60 , ASN A:71 , ALA A:73 , ALA A:74 , LYS B:9BINDING SITE FOR RESIDUE NSN A 25

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UHE)

(-) 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:97
 aligned with PAND_HELPY | P56065 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:97
                                                                                                                     117     
                                    35        45        55        65        75        85        95       105       115 |     
           PAND_HELPY    26 ITIDEDLAKLAKLREGMKVEIVDVNNGERFSTYVILGKKRGEICVNGAAARKVAIGDVVIILAYASMNEDEINAHKPSIVLVDEKNEILEKG-----   -
               SCOP domains d1uhe.1 B:,A: Pyruvoyl dependent aspartate decarboxylase, ADC                                     SCOP domains
               CATH domains 1uheA00 A:26-122  [code=2.40.40.20, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhh......eeeeee.....eeeee.eee.....eeee.hhhhhh....eeeeeeeeeehhhhhhhh..eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1uhe A  26 ITIDEDLAKLAKLREGMKVEIVDVNNGERFSTYVILGKKRGEICVNGAAARKVAIGDVVIILAYASMNEDEINAHKPSIVLVDEKNEILEKGLEHHH 122
                                    35        45        55        65        75        85        95       105       115       


Chain B from PDB  Type:PROTEIN  Length:24
 aligned with PAND_HELPY | P56065 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:24
                                    10        20    
           PAND_HELPY     1 MTFEMLYSKIHRATITDANLNYIG  24
               SCOP domains d1uhe.1 B:,A:            SCOP domains
               CATH domains ------------------------ CATH domains
           Pfam domains (1) Asp_decarbox-1uheB01     Pfam domains (1)
           Pfam domains (2) Asp_decarbox-1uheB02     Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeeee..eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                 1uhe B   1 MTFEMLYSKIHRATITDANLNYIG  24
                                    10        20
   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, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) 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_HELPY | P56065)
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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  PAND_HELPY | P56065
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  4.1.1.11
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAND_HELPY | P56065: 1uhd

(-) Related Entries Specified in the PDB File

1uhd THE SAME PROTEIN, PYRUVOLY GROUP BOUND FORM