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(-) Description

Title :  CRYSTAL STRUCTURE OF DOPA DECARBOXYLASE
 
Authors :  P. Burkhard, P. Dominici, C. Borri-Voltattorni, J. N. Jansonius, V. N. Malashkevich
Date :  16 Aug 01  (Deposition) - 26 Oct 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dopa Decarboxylase, Carbidopa, Parkinson'S Disease, Vitamin B6, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Burkhard, P. Dominici, C. Borri-Voltattorni, J. N. Jansonius, V. N. Malashkevich
Structural Insight Into Parkinson'S Disease Treatment From Drug-Inhibited Dopa Decarboxylase.
Nat. Struct. Biol. V. 8 963 2001
PubMed-ID: 11685243  |  Reference-DOI: 10.1038/NSB1101-963
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DOPA DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKDDC(DELTA)4
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organ: KIDNEY
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: AROMATIC-L-AMINO-ACID DECARBOXYLASE;
DDC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:80 , SER A:147 , ALA A:148 , SER A:149 , HIS A:192 , THR A:246 , ASP A:271 , ALA A:273 , ASN A:300 , HIS A:302 , LYS A:303 , HOH A:609 , HOH B:604BINDING SITE FOR RESIDUE PLP A 601
2AC2SOFTWAREPHE B:80 , SER B:147 , ALA B:148 , SER B:149 , HIS B:192 , THR B:246 , ASP B:271 , ALA B:273 , ASN B:300 , HIS B:302 , LYS B:303 , HOH B:620 , HOH B:624BINDING SITE FOR RESIDUE PLP B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JS6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JS6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JS6)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DDC_GAD_HDC_YDCPS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.DDC_PIG296-317
 		  2A:296-317
B:296-317

(-) Exons   (0, 0)

(no "Exon" information available for 1JS6)

(-) 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:464
 aligned with DDC_PIG | P80041 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:476
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
              DDC_PIG     1 MNASDFRRRGKEMVDYMADYLEGIEGRQVYPDVQPGYLRPLIPATAPQEPDTFEDILQDVEKIIMPGVTHWHSPYFFAYFPTASSYPAMLADMLCGAIGCIGFSWAASPACTELETVMMDWLGKMLQLPEAFLAGEAGEGGGVIQGSASEATLVALLAARTKVVRRLQAASPGLTQGAVLEKLVAYASDQAHSSVERAGLIGGVKLKAIPSDGKFAMRASALQEALERDKAAGLIPFFVVATLGTTSCCSFDNLLEVGPICHEEDIWLHVDAAYAGSAFICPEFRHLLNGVEFADSFNFNPHKWLLVNFDCSAMWVKRRTDLTGAFKLDPVYLKHSHQGSGLITDYRHWQLPLGRRFRSLKMWFVFRMYGVKGLQAYIRKHVQLSHEFEAFVLQDPRFEVCAEVTLGLVCFRLKGSDGLNEALLERINSARKIHLVPCRLRGQFVLRFAICSRKVESGHVRLAWEHIRGLAAELLA 476
               SCOP domains d1js6a_ A: DOPA decarboxylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1js6A01 A:1-81 dopa decarboxylase, N-terminal domain                             1js6A02 A:82-379 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                                                      1js6A03 A:380-476 Aspartate Aminotransferase, domain 1                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh.........hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......eeeee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhheeeeee....hhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeehhhhhh......eeeee.hhhhhhhhhh------------.....hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeeeee..hhhhhhhhhhhhhhhh....eeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1js6 A   1 MNASDFRRRGKEMVDYMADYLEGIEGRQVYPDVQPGYLRPLIPATAPQEPDTFEDILQDVEKIIMPGVTHWHSPYFFAYFPTASSYPAMLADMLCGAIGCIGFSWAASPACTELETVMMDWLGKMLQLPEAFLAGEAGEGGGVIQGSASEATLVALLAARTKVVRRLQAASPGLTQGAVLEKLVAYASDQAHSSVERAGLIGGVKLKAIPSDGKFAMRASALQEALERDKAAGLIPFFVVATLGTTSCCSFDNLLEVGPICHEEDIWLHVDAAYAGSAFICPEFRHLLNGVEFADSFNFNPHKWLLVNFDCSAMWVKRRTDLTGAFK------------SGLITDYRHWQLPLGRRFRSLKMWFVFRMYGVKGLQAYIRKHVQLSHEFEAFVLQDPRFEVCAEVTLGLVCFRLKGSDGLNEALLERINSARKIHLVPCRLRGQFVLRFAICSRKVESGHVRLAWEHIRGLAAELLA 476
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      |  -       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
                                                                                                                                                                                                                                                                                                                                                                327          340                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:464
 aligned with DDC_PIG | P80041 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:476
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
              DDC_PIG     1 MNASDFRRRGKEMVDYMADYLEGIEGRQVYPDVQPGYLRPLIPATAPQEPDTFEDILQDVEKIIMPGVTHWHSPYFFAYFPTASSYPAMLADMLCGAIGCIGFSWAASPACTELETVMMDWLGKMLQLPEAFLAGEAGEGGGVIQGSASEATLVALLAARTKVVRRLQAASPGLTQGAVLEKLVAYASDQAHSSVERAGLIGGVKLKAIPSDGKFAMRASALQEALERDKAAGLIPFFVVATLGTTSCCSFDNLLEVGPICHEEDIWLHVDAAYAGSAFICPEFRHLLNGVEFADSFNFNPHKWLLVNFDCSAMWVKRRTDLTGAFKLDPVYLKHSHQGSGLITDYRHWQLPLGRRFRSLKMWFVFRMYGVKGLQAYIRKHVQLSHEFEAFVLQDPRFEVCAEVTLGLVCFRLKGSDGLNEALLERINSARKIHLVPCRLRGQFVLRFAICSRKVESGHVRLAWEHIRGLAAELLA 476
               SCOP domains d1js6b_ B: DOPA decarboxylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1js6B01 B:1-81 dopa decarboxylase, N-terminal domain                             1js6B02 B:82-379 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                                                      1js6B03 B:380-476 Aspartate Aminotransferase, domain 1                                            CATH domains
           Pfam domains (1) ----------------------------------Pyridoxal_deC-1js6B01 B:35-414                                                                                                                                                                                                                                                                                                                                                              -------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------Pyridoxal_deC-1js6B02 B:35-414                                                                                                                                                                                                                                                                                                                                                              -------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh.........hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhheeeeee....hhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeehhhhhh......eeeee.hhhhhhhhhh------------.....hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeeeee..hhhhhhhhhhhhhhhh....eeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1js6 B   1 MNASDFRRRGKEMVDYMADYLEGIEGRQVYPDVQPGYLRPLIPATAPQEPDTFEDILQDVEKIIMPGVTHWHSPYFFAYFPTASSYPAMLADMLCGAIGCIGFSWAASPACTELETVMMDWLGKMLQLPEAFLAGEAGEGGGVIQGSASEATLVALLAARTKVVRRLQAASPGLTQGAVLEKLVAYASDQAHSSVERAGLIGGVKLKAIPSDGKFAMRASALQEALERDKAAGLIPFFVVATLGTTSCCSFDNLLEVGPICHEEDIWLHVDAAYAGSAFICPEFRHLLNGVEFADSFNFNPHKWLLVNFDCSAMWVKRRTDLTGAFK------------SGLITDYRHWQLPLGRRFRSLKMWFVFRMYGVKGLQAYIRKHVQLSHEFEAFVLQDPRFEVCAEVTLGLVCFRLKGSDGLNEALLERINSARKIHLVPCRLRGQFVLRFAICSRKVESGHVRLAWEHIRGLAAELLA 476
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      |  -       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
                                                                                                                                                                                                                                                                                                                                                                327          340
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DDC_PIG | P80041)
molecular function
    GO:0004058    aromatic-L-amino-acid decarboxylase activity    Catalysis of the reaction: L-amino acid + H+ = R-H + CO2.
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0042423    catecholamine biosynthetic process    The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0042416    dopamine biosynthetic process    The chemical reactions and pathways resulting in the formation of dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline.

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 Related Entries

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        DDC_PIG | P80041: 1js3

(-) Related Entries Specified in the PDB File

1js3 CRYSTAL STRUCTURE OF DOPA DECARBOXYLASE IN COMPLEX WITH THE INHIBITOR CARBIDOPA