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(-) Description

Title :  YEAST OXYGEN-DEPENDENT COPROPORPHYRINOGEN OXIDASE
 
Authors :  J. D. Phillips, F. G. Whitby, C. A. Warby, P. Labbe, C. Yang, J. W. Pflugrath, J. D. Ferrara, H. Robinson, J. P. Kushner, C. P. Hill
Date :  08 Jun 04  (Deposition) - 20 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Coproporphyrinogen Oxidase, Heme Biosynthesis, Enzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Phillips, F. G. Whitby, C. A. Warby, P. Labbe, C. Yang, J. W. Pflugrath, J. D. Ferrara, H. Robinson, J. P. Kushner, C. P. Hill
Crystal Structure Of The Oxygen-Dependant Coproporphyrinogen Oxidase (Hem13P) Of Saccharomyces Cerevisiae
J. Biol. Chem. V. 279 38960 2004
PubMed-ID: 15194705  |  Reference-DOI: 10.1074/JBC.M406050200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COPROPORPHYRINOGEN III OXIDASE
    Chains: A
    EC Number: 1.3.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TRUNCATED ODCPO
    Gene: HEM13, YDR044W, YD5112.02
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: COPROPORPHYRINOGENASE, COPROGEN OXIDASE, COX

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1TK1)

(-) Sites  (0, 0)

(no "Site" information available for 1TK1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TK1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:51 -Gly A:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TK1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPROGEN_OXIDASEPS01021 Coproporphyrinogen III oxidase signature.HEM6_YEAST190-214  1A:190-214

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR044W1YDR044W.1IV:546641-547627987HEM6_YEAST1-3283281A:8-265 (gaps)258

(-) Sequences/Alignments

Asymmetric/Biological 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:219
 aligned with HEM6_YEAST | P11353 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:258
                                    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        
           HEM6_YEAST     8 RNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGR 265
               SCOP domains d1tk1a_ A: Coproporphyrinogen III          oxidase                                                                                                                                                                                                                 SCOP domains
               CATH domains 1tk1A00 A:8-265 oxygen-dependent c         oproporphyrinogen oxidase                                                                                                                                                                                               CATH domains
               Pfam domains ------Coprogen_oxidas-1tk1A01 A:14         -265                                                                                                                                                                                                                    Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh........---------...eeeeee....eeeeeeeeeeeeeeehhhhhhhhhhhh.---------------..eeeeeeeeeeeeee......eeeeeeeeeee.........eeeeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhh.---------------..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         --------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:8-265 (gaps) UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                          Transcript 1
                 1tk1 A   8 RNLPIRQQMEALIRRKQAEITQGLESIDTVKFHA---------GGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHK---------------DGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKK---------------GIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGR 265
                                    17        27        37   |     -   |    57        67        77        87   |     -       107       117       127       137       147       157       167       177       187   |     -       207       217       227       237       247       257        
                                                            41        51                                      91             107                                                                                 191             207
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Coprogen_oxidas] (5)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HEM6_YEAST | P11353)
molecular function
    GO:0004109    coproporphyrinogen oxidase activity    Catalysis of the reaction: coproporphyrinogen III + 2 H(+) + O(2) = 2 CO(2) + 2 H(2)O + protoporphyrinogen IX.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006783    heme biosynthetic process    The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
    GO:0006782    protoporphyrinogen IX biosynthetic process    The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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    Gly A:51 - Gly A:52   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        HEM6_YEAST | P11353: 1tkl 1tlb 1txn

(-) Related Entries Specified in the PDB File

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