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(-) Description

Title :  T57V MUTANT OF ASPARTATE DECARBOXYLASE
 
Authors :  M. E. Webb, B. A. Yorke, T. Kershaw, S. Lovelock, C. M. C. Lobley, M. L. Kil A. G. Smith, T. L. Blundell, A. R. Pearson, C. Abell
Date :  25 Jun 12  (Deposition) - 25 Jul 12  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lyase, Amino Acid Substitution (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Webb, B. A. Yorke, T. Kershaw, S. Lovelock, C. M. C. Lobley, M. L. Kilkenny, A. G. Smith, T. L. Blundell, A. R. Pearson, C. Abell
Threonine 57 Is Required For The Post-Translational Activation Of Escherichia Coli Aspartate Alpha-Decarboxylas
Acta Crystallogr. , Sect. D V. 70 1166 2014
PubMed-ID: 24699660  |  Reference-DOI: 10.1107/S1399004713034275

(-) Compounds

Molecule 1 - ASPARTATE 1-DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C41
    Expression System Vector: PDKS1
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: L-ASPARTATE-ALPHA-DECARBOXYLASE, ASPARTATE ALPHA-DECARBOXYLASE, ASPARTATE 1-DECARBOXYLASE BETA CHAIN, ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MLI4Ligand/IonMALONATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MLI8Ligand/IonMALONATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:9 , HIS A:11 , TRP A:47 , ARG A:54 , ILE A:86 , VAL B:57 , TYR B:58 , ASN B:72 , GLY B:73 , ALA B:74 , ALA B:75 , HOH B:2014BINDING SITE FOR RESIDUE MLI B1118
2AC2SOFTWAREVAL A:57 , TYR A:58 , ASN A:72 , GLY A:73 , ALA A:74 , ALA A:75 , HOH A:2027 , LYS B:9 , HIS B:11 , TRP B:47 , ARG B:54 , ILE B:86BINDING SITE FOR RESIDUE MLI A1118
3AC3SOFTWAREARG A:12 , VAL A:49 , THR A:50 , ILE A:84 , HOH A:2039 , HIS B:21 , ARG B:102BINDING SITE FOR RESIDUE MLI A1119
4AC4SOFTWARESER A:25 , ASN A:41 , TYR A:58 , ILE A:60 , HOH A:2026 , PRO B:103BINDING SITE FOR RESIDUE MLI A1120

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val A:-4 -Pro A:-3

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AZD)

(-) 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:122
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:122
                                 1                                                                                                                    
                                 |   5        15        25        35        45        55        65        75        85        95       105       115  
           PAND_ECOLI     - -----MIRTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRT 117
               SCOP domains d4azda_ A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeeee..eee......eeeehhhhhhhh.....eeeeee.....eeeeeeeee......eeee.hhhhh.....eeeeeeeeeeehhhhhh...eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4azd A  -4 VPRGSMIRTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSVYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRT 117
                                     5        15        25        35        45        55        65        75        85        95       105       115  


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           PAND_ECOLI     1 MIRTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRT 117
               SCOP domains d4azdb_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee...........eeeehhhhhhhh.....eeeeee.....eeeeeeeee......ee.hhhhhhh.....eeeeeeeeeeehhhhh....eeeeee...ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4azd B   1 MIRTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSVYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRT 117
                                    10        20        30        40        50        60        70        80        90       100       110
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  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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  4.1.1.11
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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 4aok 4aon 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
4aok CONFORMATIONAL DYNAMICS OF ASPARTATE ALPHA-DECARBOXYLASE ACTIVE SITE REVEALED BY PROTEIN-LIGAND COMPLEXES: 1- METHYL-L-ASPARTATE COMPLEX
4aon CONFORMATIONAL DYNAMICS OF ASPARTATE ALPHA-DECARBOXYLASE ACTIVE SITE REVEALED BY PROTEIN-LIGAND COMPLEXES: 1- METHYL-L-ASPARTATE COMPLEX