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(-) Description

Title :  CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE FORMATE COMPLEX
 
Authors :  R. Anand, P. C. Dorrestein, C. Kinsland, T. P. Begley, S. E. Ealick
Date :  27 Feb 02  (Deposition) - 03 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Oxalate, Decarboxylase, Formate, Manganese, Cupin, 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: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YVRK
    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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2MG1Ligand/IonMAGNESIUM ION
3MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1FMT12Ligand/IonFORMIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:95 , HIS A:97 , GLU A:101 , HIS A:140 , FMT A:550BINDING SITE FOR RESIDUE MN A 500
2AC2SOFTWAREHIS A:273 , HIS A:275 , GLU A:280 , HIS A:319 , GLU A:333 , HOH A:891 , HOH A:895BINDING SITE FOR RESIDUE MN A 501
3AC3SOFTWAREHIS A:174 , FMT A:650 , HOH A:1033 , HOH A:1034BINDING SITE FOR RESIDUE MG A 502
4AC4SOFTWAREMET 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:976BINDING SITE FOR RESIDUE FMT A 550
5AC5SOFTWAREGLU A:39 , MG A:502BINDING SITE FOR RESIDUE FMT A 650

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L3J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L3J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L3J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L3J)

(-) Exons   (0, 0)

(no "Exon" information available for 1L3J)

(-) 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 d1l3ja_ A: Oxalate decarboxylase OxdC (YvrK)                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1l3jA01 A:8-55,A:230-379 Jelly Rolls            1l3jA02 A:56-229 Jelly Rolls                                                                                                                                                  1l3jA01 A:8-55,A:230-379 Jelly Rolls                                                                                                                   CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1l3jA01 A:228-366                                                                                                                  ------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1l3jA02 A:228-366                                                                                                                  ------------- Pfam domains (2)
         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....eeeeee.....eeeeeee.eeeeeeeee..eeeeeeee...eeee.....eeeee.....eeeeeee.......eehhhhhhh.hhhhhhhhhh.hhhhhh........ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l3j 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
   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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OXDC_BACSU | O34714: 1j58 1uw8 2uy8 2uy9 2uya 2uyb 2v09 3s0m 4met 5hi0

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