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 :  ACETOLACTATE DECARBOXYLASE WITH A BOUND GLYCEROL
 
Authors :  V. A Marlow, D. Rea, S. Najmudin, M. Wills, V. Fulop
Date :  12 Jun 13  (Deposition) - 11 Sep 13  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Lyase, Acetoin Biosynthesis, Stereoselective Decarboxylation, Bifunctional Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Marlow, D. Rea, S. Najmudin, M. Wills, V. Fulop
Structure And Mechanism Of Acetolactate Decarboxylase.
Acs Chem. Biol. V. 8 2339 2013
PubMed-ID: 23985082  |  Reference-DOI: 10.1021/CB400429H

(-) Compounds

Molecule 1 - ALPHA-ACETOLACTATE DECARBOXYLASE
    Atcc: 11031
    Chains: A
    EC Number: 4.1.1.5
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PJA199
    Expression System Strain: JA222
    Expression System Taxid: 1423
    Expression System Variant: TOC46
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 29-285
    Organism Scientific: BREVIBACILLUS BREVIS
    Organism Taxid: 1393
    Synonym: ALDC, ACETOLACTATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:194 , HIS A:196 , HIS A:207 , GLU A:253 , GOL A:1258BINDING SITE FOR RESIDUE ZN A 1257
2AC2SOFTWAREGLU A:65 , ARG A:145 , VAL A:147 , HIS A:194 , HIS A:196 , HIS A:207 , GLU A:253 , ZN A:1257BINDING SITE FOR RESIDUE GOL A 1258
3AC3SOFTWARELYS A:140 , GLU A:200 , LYS A:202 , ASP A:214 , HOH A:2171 , HOH A:2327 , HOH A:2328BINDING SITE FOR RESIDUE GOL A 1259
4AC4SOFTWAREPRO A:148 , GLN A:150 , PRO A:155 , GLU A:159 , HOH A:2153 , HOH A:2230 , HOH A:2231BINDING SITE FOR RESIDUE GOL A 1260
5AC5SOFTWARELEU A:36 , GLY A:37 , GLN A:38 , ARG A:152 , TYR A:154 , HOH A:2031 , HOH A:2146 , HOH A:2221BINDING SITE FOR RESIDUE GOL A 1261

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BT6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:152 -Pro A:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BT6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BT6)

(-) Exons   (0, 0)

(no "Exon" information available for 4BT6)

(-) 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:237
 aligned with ALDC_BREBE | P23616 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:237
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       
           ALDC_BREBE    48 APKNVLFQYSTINALMLGQFEGDLTLKDLKLRGDMGLGTINDLDGEMIQMGTKFYQIDSTGKLSELPESVKTPFAVTTHFEPKEKTTLTNVQDYNQLTKMLEEKFENKNVFYAVKLTGTFKMVKARTVPKQTRPYPQLTEVTKKQSEFEFKNVKGTLIGFYTPNYAAALNVPGFHLHFITEDKTSGGHVLNLQFDNANLEISPIHEFDVQLPHTDDFAHSDLTQVTTSQVHQAESER 284
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhh......eehhhhhhhh.eeee.hhhhh.eeeee..eeeee.....eee.....ee..eee......eeeeeeee.hhhhhhhhhhhhhh....eeeeeeeeeeeeeeeee.........hhhhhhh..eeeeeeeeeeeeeeeeehhhhh.....eeeeeeee.....eeeeeeeeeeeeeeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bt6 A  20 APKNVLFQYSTINALMLGQFEGDLTLKDLKLRGDMGLGTINDLDGEMIQMGTKFYQIDSTGKLSELPESVKTPFAVTTHFEPKEKTTLTNVQDYNQLTKMLEEKFENKNVFYAVKLTGTFKMVKARTVPKQTRPYPQLTEVTKKQSEFEFKNVKGTLIGFYTPNYAAALNVPGFHLHFITEDKTSGGHVLNLQFDNANLEISPIHEFDVQLPHTDDFAHSDLTQVTTSQVHQAESER 256
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
   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 4BT6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BT6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BT6)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (ALDC_BREBE | P23616)
molecular function
    GO:0047605    acetolactate decarboxylase activity    Catalysis of the reaction: (S)-2-hydroxy-2-methyl-3-oxobutanoate = (R)-2-acetoin + 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:0045151    acetoin biosynthetic process    The chemical reactions and pathways resulting in the formation of acetoin, 3-hydroxy-2-butanone.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:152 - Pro A:153   [ 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
  4bt6
    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
  ALDC_BREBE | P23616
    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)
  4.1.1.5
    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
  ALDC_BREBE | P23616
    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
        ALDC_BREBE | P23616: 4bt2 4bt3 4bt4 4bt5 4bt7

(-) Related Entries Specified in the PDB File

4bt2 ACETOLACTATE DECARBOXYLASE WITH A BOUND 1,2-ETHANEDIOL
4bt3 ACETOLACTATE DECARBOXYLASE WITH A BOUND (2R,3R)-2,3- DIHYDROXY-2- METHYLBUTANOIC ACID
4bt4 ACETOLACTATE DECARBOXYLASE WITH A BOUND (2S,3S)-2,3- DIHYDROXY-2- METHYLBUTANOIC ACID
4bt5 ACETOLACTATE DECARBOXYLASE WITH A BOUND (2S,3R)-2,3- DIHYDROXY-2- METHYLBUTANOIC ACID
4bt7 ACETOLACTATE DECARBOXYLASE WITH A BOUND PHOSPHATE ION