Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURES OF THE WILD-TYPE, MUTANT-P1A AND INACTIVATED MALONATE SEMIALDEHYDE DECARBOXYLASE: A STRUCTURAL BASIS FOR THE DECARBOXYLASE AND HYDRATASE ACTIVITIES
 
Authors :  J. J. Almrud, G. J. Poelarends, W. H. Johnson Jr. , H. Serrano, M. L. Hack C. P. Whitman
Date :  13 Jul 05  (Deposition) - 22 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Tautomerase Superfamily; Beta-Alpha-Beta; Homotrimeric, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Almrud, G. J. Poelarends, W. H. Johnson Jr. , H. Serrano, M. L. Hackert, C. P. Whitman
Crystal Structures Of The Wild-Type, P1A Mutant, And Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis For The Decarboxylase And Hydratase Activities
Biochemistry V. 44 14818 2005
PubMed-ID: 16274229  |  Reference-DOI: 10.1021/BI051383M

(-) Compounds

Molecule 1 - MALONATE SEMIALDEHYDE DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ORF130
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PAVONACEAE
    Organism Taxid: 47881
    Strain: 170

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AAJ)

(-) Sites  (0, 0)

(no "Site" information available for 2AAJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AAJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AAJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AAJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AAJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2AAJ)

(-) 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:129
 aligned with Q9EV83_PSEPV | Q9EV83 from UniProtKB/TrEMBL  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q9EV83_PSEPV     2 PLLKFDIFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 130
               SCOP domains d2aaja1 A:1-129 Malonate semialdehyde decarboxylase, MSAD                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhh...............eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhhhh......hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aaj A   1 ALLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSESQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with Q9EV83_PSEPV | Q9EV83 from UniProtKB/TrEMBL  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q9EV83_PSEPV     2 PLLKFDIFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 130
               SCOP domains d2aajb_ B: Malonate semialdehyde decarboxylase, MSAD                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhh...............eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhhhh......hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aaj B   1 ALLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSESQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 129
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AAJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AAJ)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9EV83_PSEPV | Q9EV83)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.

 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
(no "Ligands, Modified Residues, Ions" information available for 2aaj)
 
  Sites
(no "Sites" information available for 2aaj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2aaj)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 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
  2aaj
    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
  Q9EV83_PSEPV | Q9EV83
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.-
    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
  Q9EV83_PSEPV | Q9EV83
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9EV83_PSEPV | Q9EV83: 2aag 2aal

(-) Related Entries Specified in the PDB File

2aag 2aal