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(-) Description

Title :  GLYCINE 24 TO SERINE MUTATION OF ASPARTATE DECARBOXYLASE
 
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 :  18 Jun 03  (Deposition) - 18 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Pyruvoyl-Dependent Decarboxylase, Intramolecular Protein Self- Processing, 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
    Chains: A, B
    EC Number: 4.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRESTA
    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

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CSX2Mod. Amino AcidS-OXY CYSTEINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CSX4Mod. Amino AcidS-OXY CYSTEINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:9 , HIS A:11 , ARG A:12 , ILE A:86 , GLU B:23 , SER B:24BINDING SITE FOR RESIDUE SO4 A 237
2AC2SOFTWAREGLU A:23 , SER A:24 , HOH A:328 , LYS B:9 , HIS B:11 , ARG B:12 , ILE B:86BINDING SITE FOR RESIDUE SO4 B 238

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PQF)

(-) 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:127
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:127
                                1                                                                                                                          
                                |    6        16        26        36        46        56        66        76        86        96       106       116       
           PAND_ECOLI     - ----MIRTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRTAKAIPV 123
               SCOP domains d1pqfa_ A: Pyruvoyl dependent aspartate decarboxylase, ADC                                                                      SCOP domains
               CATH domains 1pqfA00 A:-3-123  [code=2.40.40.20, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeee..eee.....eeeeehhhhhhhh.....eeeeee.....eeeeeeeee......eeee.hhhhh.....eeeeeeeeeeehhhhhhh..eeeeee...eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pqf A  -3 PRGSMIRTMLQGKLHRVKVTHADLHYESSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHcASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRTAKAIPV 123
                                     6        16        26        36        46        56        66        76 |      86        96       106       116       
                                                                                                            78-CSX                                         


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
           PAND_ECOLI     1 MIRTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKR 116
               SCOP domains d1pqfb_ B: Pyruvoyl dependent aspartate decarboxylase, ADC                                                           SCOP domains
               CATH domains 1pqfB00 B:1-116  [code=2.40.40.20, no name defined]                                                                  CATH domains
           Pfam domains (1) Asp_decarbox-1pqfB01 B:1-116                                                                                         Pfam domains (1)
           Pfam domains (2) Asp_decarbox-1pqfB02 B:1-116                                                                                         Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeee...........eeeehhhhhhhh.....eeeeee.....eeeeeeeee......eee.hhhhhh.....eeeeeeeeeeehhhhh....eee.ee...ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1pqf B   1 MIRTMLQGKLHRVKVTHADLHYESSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHcASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKR 116
                                    10        20        30        40        50        60        70       |80        90       100       110      
                                                                                                        78-CSX
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1aw8 1ppy 1pqe 1pqh 1pt0 1pt1 1pyq 1pyu