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 :  DEL162-163 MUTANT OF BACILLUS SUBTILIS OXALATE DECARBOXYLASE OXDC
 
Authors :  V. J. Just, M. R. Burrell, L. Bowater, I. Mcrobbie, C. E. M. Stevenson, D. M. Lawson, S. Bornemann
Date :  03 Apr 07  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Lyase, Cupin, Formate, Oxalate, Manganese, Metal Binding Protein, Metal-Binding, Decarboxylase, Del162-163 Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. J. Just, M. R. Burrell, L. Bowater, I. Mcrobbie, C. E. M. Stevenson, D. M. Lawson, S. Bornemann
The Identity Of The Active Site Of Oxalate Decarboxylase And The Importance Of The Stability Of Active-Site Lid Conformations.
Biochem. J. V. 407 397 2007
PubMed-ID: 17680775  |  Reference-DOI: 10.1042/BJ20070708

(-) Compounds

Molecule 1 - OXALATE DECARBOXYLASE OXDC
    Atcc: 23857
    Chains: A
    EC Number: 4.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLB36
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET32A
    Fragment: RESIDUES 1-161,164-385
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MN2Ligand/IonMANGANESE (II) ION
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4TRS6Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:95 , HIS A:97 , GLU A:101 , HIS A:140 , HOH A:2405 , HOH A:2406BINDING SITE FOR RESIDUE MN A1383
2AC2SOFTWAREHIS A:273 , HIS A:275 , GLU A:280 , HIS A:319 , GLU A:333 , HOH A:2407BINDING SITE FOR RESIDUE MN A1384
3AC3SOFTWAREGLU A:117 , PRO A:135 , SER A:136 , ASN A:277 , HIS A:339 , ALA A:341 , HOH A:2408 , HOH A:2409 , HOH A:2410BINDING SITE FOR RESIDUE TRS A1385
4AC4SOFTWAREGLY A:43 , HIS A:56 , ARG A:58 , HOH A:2411BINDING SITE FOR RESIDUE GOL A1386
5AC5SOFTWAREARG A:92 , HOH A:2149 , HOH A:2255 , HOH A:2406BINDING SITE FOR RESIDUE CL A1387

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UYA)

(-) 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:375
 aligned with OXDC_BACSU | O34714 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:377
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       
           OXDC_BACSU     6 DIPQPIRGDKGATVKIPRNIERDRQNPDMLVPPETDHGTVSNMKFSFSDTHNRLEKGGYAREVTVRELPISENLASVNMRLKPGAIRELHWHKEAEWAYMIYGSARVTIVDEKGRSFIDDVGEGDLWYFPSGLPHSIQALEEGAEFLLVFDDGSFSENSTFQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIVEGPNGEVPYPFTYRLLEQEPIESEGGKVYIADSTNFKVSKTIASALVTVEPGAMRELHWHPNTHEWQYYISGKARMTVFASDGHARTFNYQAGDVGYVPFAMGHYVENIGDEPLVFLEIFKDDHYADVSLNQWLAMLPETFVQAHLDLGKDFTDVLSKEKHPVVKKK 382
               SCOP domains d2uyaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2uyaA01 A:6-55,A:230-382 Jelly Rolls              2uyaA02 A:56-229 Jelly Rolls                                                                                                                                                  2uyaA01 A:6-55,A:230-382 Jelly Rolls                                                                                                                      CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-2uyaA01 A:228-366                                                                                                                  ---------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-2uyaA02 A:228-366                                                                                                                  ---------------- Pfam domains (2)
         Sec.struct. author .....ee..ee.......hhhhhhhhhhhhh............eee.hhh..eee..eeeeee...........eeeeeee....eeeeee....eeeeeeeeeeeeeee........................eeeeeeeeeeeeeeee......--....hhhhhhh.hhhhhhhhhh..hhhhh................hhhhhh................hhh..eee..eeeeee...........eeeeeee...eeeeeee.....eeeeeee.eeeeeeeee..eeeeeeee..eeeee.....eeeee.....eeeeeee.......eehhhhhhh.hhhhhhhhhh.hhhhhh........eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uya A   6 DIPQPIRGDKGATVKIPRNIERDRQNPDMLVPPETDHGTVSNMKFSFSDTHNRLEKGGYAREVTVRELPISENLASVNMRLKPGAIRELHWHKEAEWAYMIYGSARVTIVDEKGRSFIDDVGEGDLWYFPSGLPHSIQALEEGAEFLLVFDDGSFS--STFQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIVEGPNGEVPYPFTYRLLEQEPIESEGGKVYIADSTNFKVSKTIASALVTVEPGAMRELHWHPNTHEWQYYISGKARMTVFASDGHARTFNYQAGDVGYVPFAMGHYVENIGDEPLVFLEIFKDDHYADVSLNQWLAMLPETFVQAHLDLGKDFTDVLSKEKHPVVKKK 382
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155     | 165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       
                                                                                                                                                                                     161  |                                                                                                                                                                                                                          
                                                                                                                                                                                        164
   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, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (OXDC_BACSU | O34714)
molecular function
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.
    GO:0046564    oxalate decarboxylase activity    Catalysis of the reaction: H(+) + oxalate = CO(2) + formate.
biological process
    GO:0033609    oxalate metabolic process    The chemical reactions and pathways involving oxalate, the organic acid ethanedioate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ 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
(no "Cis Peptide Bonds" information available for 2uya)
 
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
  2uya
    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
  OXDC_BACSU | O34714
    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)
  4.1.1.2
    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
  OXDC_BACSU | O34714
    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
        OXDC_BACSU | O34714: 1j58 1l3j 1uw8 2uy8 2uy9 2uyb 2v09 3s0m 4met 5hi0

(-) Related Entries Specified in the PDB File

1j58 CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE
1l3j CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE FORMATE COMPLEX
1uw8 CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE
2uy9 E162A MUTANT OF BACILLUS SUBTILIS OXALATE DECARBOXYLASE OXDC
2uyb S161A MUTANT OF BACILLUS SUBTILIS OXALATE DECARBOXYLASE OXDC