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 :  CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE
 
Authors :  R. Anand, P. C. Dorrestein, C. Kinsland, T. P. Begley, S. E. Ealick
Date :  25 Feb 02  (Deposition) - 03 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Cupin, Decarboxyklase, Oxalate, Manganese, Formate, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Anand, P. C. Dorrestein, C. Kinsland, T. P. Begley, S. E. Ealick
Structure Of Oxalate Decarboxylase From Bacillus Subtilis A 1. 75 A Resolution.
Biochemistry V. 41 7659 2002
PubMed-ID: 12056897  |  Reference-DOI: 10.1021/BI0200965

(-) Compounds

Molecule 1 - YVRK PROTEIN
    Chains: A
    Engineered: YES
    Expression System: BACTERIA
    Expression System Common: EUBACTERIA
    Expression System Plasmid: PET16B
    Expression System Taxid: 2
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: OXALATE DECARBOXYLASE

 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, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MG1Ligand/IonMAGNESIUM ION
3MN2Ligand/IonMANGANESE (II) ION
4MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 54)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3MN-1Ligand/IonMANGANESE (II) ION
4MSE48Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:95 , HIS A:97 , GLU A:101 , HIS A:140 , FMT A:550 , HOH A:697BINDING SITE FOR RESIDUE MN A 500
2AC2SOFTWAREHIS A:273 , HIS A:275 , GLU A:280 , HIS A:319 , GLU A:333 , HOH A:579 , HOH A:634BINDING SITE FOR RESIDUE MN A 501
3AC3SOFTWAREHIS A:42 , HIS A:174BINDING SITE FOR RESIDUE MG A 502
4AC4SOFTWAREMSE A:84 , ARG A:92 , HIS A:95 , HIS A:97 , GLU A:101 , LEU A:153 , PHE A:155 , MN A:500 , HOH A:697 , HOH A:765BINDING SITE FOR RESIDUE FMT A 550

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J58)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J58)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J58)

(-) Exons   (0, 0)

(no "Exon" information available for 1J58)

(-) 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:372
 aligned with OXDC_BACSU | O34714 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:372
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377  
           OXDC_BACSU     8 PQPIRGDKGATVKIPRNIERDRQNPDMLVPPETDHGTVSNMKFSFSDTHNRLEKGGYAREVTVRELPISENLASVNMRLKPGAIRELHWHKEAEWAYMIYGSARVTIVDEKGRSFIDDVGEGDLWYFPSGLPHSIQALEEGAEFLLVFDDGSFSENSTFQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIVEGPNGEVPYPFTYRLLEQEPIESEGGKVYIADSTNFKVSKTIASALVTVEPGAMRELHWHPNTHEWQYYISGKARMTVFASDGHARTFNYQAGDVGYVPFAMGHYVENIGDEPLVFLEIFKDDHYADVSLNQWLAMLPETFVQAHLDLGKDFTDVLSKEKHPVV 379
               SCOP domains d1j58a_ A: Oxalate decarboxylase OxdC (YvrK)                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1j58A01 A:8-55,A:230-379 Jelly Rolls            1j58A02 A:56-229 Jelly Rolls                                                                                                                                                  1j58A01 A:8-55,A:230-379 Jelly Rolls                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..ee.......hhhhhhhhhhhhh............eehhhhh..eee..eeeeee...........eeeeeee....eeeeeee...eeeeeeeeeeeeeee.....eeeeeee..eeeee.....eeeeeeeeeeeeeeee.....hhh.eeehhhhhhh.hhhhhhhhhh..hhhhh........ee......hhhhhh............eee.hhh..ee...eeeeee...........eeeeeee...............eeeeeee.eeeeeeeee..eeeeeeee...eeee.....eeeee.....eeeeeee.......eehhhhhhh.hhhhhhhhhh.hhhhhh........ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j58 A   8 PQPIRGDKGATVKIPRNIERDRQNPDmLVPPETDHGTVSNmKFSFSDTHNRLEKGGYAREVTVRELPISENLASVNmRLKPGAIRELHWHKEAEWAYmIYGSARVTIVDEKGRSFIDDVGEGDLWYFPSGLPHSIQALEEGAEFLLVFDDGSFSENSTFQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIVEGPNGEVPYPFTYRLLEQEPIESEGGKVYIADSTNFKVSKTIASALVTVEPGAmRELHWHPNTHEWQYYISGKARmTVFASDGHARTFNYQAGDVGYVPFAmGHYVENIGDEPLVFLEIFKDDHYADVSLNQWLAmLPETFVQAHLDLGKDFTDVLSKEKHPVV 379
                                    17        27      | 37        47|       57        67        77      | 87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267 |     277       287   |   297       307       317       327       337       347   |   357       367       377  
                                                     34-MSE        48-MSE                              84-MSE              105-MSE                                                                                                                                                             269-MSE               291-MSE                   317-MSE                           351-MSE
   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  (0, 0)

(no "Pfam Domain" information available for 1J58)

(-) 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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1j58)
 
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
  1j58
    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)
  (no 'Enzyme Classificator' available)
    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: 1l3j 1uw8 2uy8 2uy9 2uya 2uyb 2v09 3s0m 4met 5hi0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1J58)