Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) 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 :  29 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, 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-ALPHA-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: 511693
 
Molecule 2 - ASPARTATE-ALPHA-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: 511693
    Other Details: POSTTRANSLATIONAL MAIN CHAIN BREAK BETWEEN CHAIN A GLY24 AND CHAIN B SER25. SAME FOR CHAINS C AND D. 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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GLU2Mod. Amino AcidGLUTAMIC ACID
2PYR2Mod. Amino AcidPYRUVIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GLU4Mod. Amino AcidGLUTAMIC ACID
2PYR4Mod. Amino AcidPYRUVIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:22 , GLY A:24 , PYR B:25 , SER B:25 , THR B:57 , TYR B:58 , GLY B:73 , ALA B:74 , ALA B:75 , LYS D:9 , HIS D:11 , TRP E:47 , ARG E:54 , ILE E:86BINDING SITE FOR RESIDUE GLU B1123
2AC2SOFTWARELYS A:9 , HIS A:11 , TRP B:47 , ARG B:54 , ILE B:86 , TYR D:22 , PYR E:25 , SER E:25 , THR E:57 , TYR E:58 , ASN E:72 , GLY E:73 , ALA E:74 , ALA E:75BINDING SITE FOR RESIDUE GLU E1116

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala B:118 -Lys B:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AON)

(-) 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: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
                4aon A   -2 RGSMIRTMLQGKLHRVKVTHADLHYEG   24
                                     7        17       


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:101
                                    33        43        53        63        73        83        93       103       113       123 
          PAND_ECOLI     24 GSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRTAKAIPVQ  124
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhh.....eeeeee.....eeeeeeeee......eeee.hhhhh.....eeeeeeeeeeehhhhhhh..eeeeee...eee.......-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                4aon B   25 sSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRTAKAIP-E 1123
                            |       33        43        53        63        73        83        93       103       113        |-|
                           25-PYR                                                                                           122 |
                                                                                                                             1123


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
                4aon D    0 SMIRTMLQGKLHRVKVTHADLHYEG   24
                                     9        19     


Chain E from PDB  Type:PROTEIN  Length:93
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:93
                                    33        43        53        63        73        83        93       103       113   
          PAND_ECOLI     24 GSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKR  116
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhh.....eeeeee.....eeeeeeeee......eeee.hhhhh.....eeeeeeeeeeehhhhh....eeeeee...ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                4aon E   25 sSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKE 1116
                            |       33        43        53        63        73        83        93       103       113 ||
                           25-PYR                                                                                    115|
                                                                                                                     1116
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GLU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PYR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala B:118 - Lys B:119   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4aon
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PAND_ECOLI | P0A790
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.11
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PAND_ECOLI | P0A790
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 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
4aok CONFORMATIONAL DYNAMICS OF ASPARTATE ALPHA-DECARBOXYLASE ACTIVE SITE REVEALED BY PROTEIN-LIGAND COMPLEXES: 1- METHYL-L-ASPARTATE COMPLEX