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(-) Description

Title :  CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE
 
Authors :  V. J. Just, C. E. M. Stevenson, L. Bowater, A. Tanner, D. M. Lawson, S. Bor
Date :  02 Feb 04  (Deposition) - 19 Feb 04  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Metal Binding Protein, Cupin, Decarboxylase, Oxalate, Manganese, Formate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. J. Just, C. E. M. Stevenson, L. Bowater, A. Tanner, D. M. Lawson, S. Bornemann
A Closed Conformation Of Bacillus Subtilis Oxalate Decarboxylase Oxdc Provides Evidence For The True Identity Of The Active Site
J. Biol. Chem. V. 279 19867 2004
PubMed-ID: 14871895  |  Reference-DOI: 10.1074/JBC.M313820200
(for further references see the PDB file header)

(-) 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: PAT1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PT7.5
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Other Details: FORMERLY KNOWN AS YVRK
    Strain: 168
    Synonym: OXDC

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TRS6Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:95 , HIS A:97 , GLU A:101 , HIS A:140 , HOH A:2397 , HOH A:2398BINDING SITE FOR RESIDUE MN A1383
2AC2SOFTWAREHIS A:273 , HIS A:275 , GLU A:280 , HIS A:319 , GLU A:333 , HOH A:2399BINDING 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:2400 , HOH A:2401 , HOH A:2402BINDING SITE FOR RESIDUE TRS A1385

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UW8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UW8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UW8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UW8)

(-) Exons   (0, 0)

(no "Exon" information available for 1UW8)

(-) 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:377
 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 d1uw8a_ A: Oxalate decarboxylase OxdC (YvrK)                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --1uw8A01 A:8-55,A:230-379 Jelly Rolls            1uw8A02 A:56-229 Jelly Rolls                                                                                                                                                  1uw8A01 A:8-55,A:230-379 Jelly Rolls                                                                                                                  --- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1uw8A01 A:228-366                                                                                                                  ---------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1uw8A02 A:228-366                                                                                                                  ---------------- Pfam domains (2)
         Sec.struct. author .....ee..ee.......hhhhhhhhhhhhh............eee.hhh..eee..eeeeee...........eeeeeee....eeeeee....eeeeeeeeeeeeeee........................eeeeeeeeeeeeeeee.....hhhhh..hhhhhhh.hhhhhhhhhh..hhhhh................hhhhhh................hhh..eee..eeeeee...........eeeeeee...eeeeeee.....eeeeeee.eeeeeeeee..eeeeeeee..eeeee....eeeeee.....eeeeeee.......eehhhhhhh.hhhhhhhhhh.hhhhhh........eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uw8 A   6 DIPQPIRGDKGATVKIPRNIERDRQNPDMLVPPETDHGTVSNMKFSFSDTHNRLEKGGYAREVTVRELPISENLASVNMRLKPGAIRELHWHKEAEWAYMIYGSARVTIVDEKGRSFIDDVGEGDLWYFPSGLPHSIQALEEGAEFLLVFDDGSFSENSTFQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIVEGPNGEVPYPFTYRLLEQEPIESEGGKVYIADSTNFKVSKTIASALVTVEPGAMRELHWHPNTHEWQYYISGKARMTVFASDGHARTFNYQAGDVGYVPFAMGHYVENIGDEPLVFLEIFKDDHYADVSLNQWLAMLPETFVQAHLDLGKDFTDVLSKEKHPVVKKK 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
   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)
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  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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OXDC_BACSU | O34714: 1j58 1l3j 2uy8 2uy9 2uya 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