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(-) Description

Title :  CONFORMATIONAL DYNAMICS OF ASPARTATE ALPHA-DECARBOXYLASE ACTIVE SITE REVEALED BY PROTEIN-LIGAND COMPLEXES: 1-METHYL-L-ASPARTATE COMPLEX
 
Authors :  B. A. Yorke, D. C. F. Monteiro, A. R. Pearson, M. E. Webb
Date :  28 Mar 12  (Deposition) - 31 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B,D,E  (2x)
Keywords :  Hydrolase, Aspartate Decarboxylase, Amino Acid Metabolism, Protein-Derived Cofactor. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Yorke, D. C. F. Monteiro, A. R. Pearson, M. E. Webb
Conformational Dynamics Of Aspartate Alpha Decarboxylase Active Site Revealed By Protein-Ligand Complexes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ASPARTATE 1-DECARBOXYLASE BETA CHAIN
    Chains: A, D
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: STAR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN
 
Molecule 2 - ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN
    Chains: B, E
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: STAR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: POSTTRANSLATIONAL MAIN CHAIN BREAK BETWEEN CHAIN A GLY24 AND CHAIN B SER25. SAME FOR CHAINS D AND E. SERINE 25 MODIFIED TO YIELD A PYRUVOYL COFACTOR IN BOTH CASES. IN THIS STRUCTURE THE BOUND LIGAND HAS FORMED A COVALENT IMINIUM INTERMEDIATE WITH PYR 25 IN BOTH SUBUNITS IN THE ASYMMETRIC UNIT.
    Synonym: ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
13A52Mod. Amino Acid(2Z,4S)-3-AZA-5-CARBOXYL-2-METHYL-4(METHYLCARBOXY)PENT-2-ENOYL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
13A54Mod. Amino Acid(2Z,4S)-3-AZA-5-CARBOXYL-2-METHYL-4(METHYLCARBOXY)PENT-2-ENOYL

(-) Sites  (0, 0)

(no "Site" information available for 4AOK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AOK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AOK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AOK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AOK)

(-) Exons   (0, 0)

(no "Exon" information available for 4AOK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:27
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:27
                               1                       
                               |     7        17       
           PAND_ECOLI     - ---MIRTMLQGKLHRVKVTHADLHYEG  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
                 4aok A  -2 RGSMIRTMLQGKLHRVKVTHADLHYEG  24
                                     7        17       


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:99
                                    34        44        54        64        74        84        94       104       114         
           PAND_ECOLI    25 SCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRTAKAIPV 123
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhh.....eeeeee.....eeeee.eee......eeee.hhhhh.....eeeeeeeeeeehhhhhhh..eeeeee...eee.hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4aok B  25 sCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRTAKAIPV 123
                            |       34        44        54        64        74        84        94       104       114         
                           25-3A5                                                                                              


Chain D from PDB  Type:PROTEIN  Length:25
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:25
                             1                       
                             |       9        19     
           PAND_ECOLI     - -MIRTMLQGKLHRVKVTHADLHYEG  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
                 4aok D   0 SMIRTMLQGKLHRVKVTHADLHYEG  24
                                     9        19     


Chain E 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 -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhh.....eeeeee.....eeeee.eee......eeee.hhhhh.....eeeeeeeeeeehhhhh....eeeeee...ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4aok E  25 sCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKR 116
                            |       34        44        54        64        74        84        94       104       114  
                           25-3A5
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4AOK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AOK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AOK)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D,E   (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 1pyu 3tm7 4aon 4azd 4cry 4crz 4cs0 4d7z

(-) Related Entries Specified in the PDB File

1aw8 PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE
1ppy NATIVE PRECURSOR OF PYRUVOYL DEPENDENT ASPARTATEDECARBOXYLASE
1pqe S25A MUTANT OF PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE
1pqf GLYCINE 24 TO SERINE MUTATION OF ASPARTATE DECARBOXYLASE
1pqh SERINE 25 TO THREONINE MUTATION OF ASPARTATE DECARBOXYLASE
1pt0 UNPROCESSED PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE WITHAN ALANINE INSERTION AT POSITION 26
1pt1 UNPROCESSED PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE WITHHISTIDINE 11 MUTATED TO ALANINE
1pyq UNPROCESSED ASPARTATE DECARBOXYLASE MUTANT
1pyu PROCESSED ASPARTATE DECARBOXYLASE MUTANT
4aon CONFORMATIONAL DYNAMICS OF ASPARTATE ALPHA-DECARBOXYLASE ACTIVE SITE REVEALED BY PROTEIN-LIGAND COMPLEXES: 1- METHYL-L-ASPARTATE COMPLEX