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Asym./Biol. Unit  (Jmol Viewer)

(-) 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 :  2.00
Chains :  Asym./Biol. Unit :  A,B
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, B
    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
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1TKL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:50 -Gly A:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPROGEN_OXIDASEPS01021 Coproporphyrinogen III oxidase signature.HEM6_YEAST190-214
 		  2A:190-214
B:190-214

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR044W1YDR044W.1IV:546641-547627987HEM6_YEAST1-3283282A:4-328
B:4-328		325
325

(-) 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:325
 aligned with HEM6_YEAST | P11353 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:325
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323     
           HEM6_YEAST     4 PQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILMSLPEHASWLYNHHPAPGSREAKLLEVTTKPREWVK 328
               SCOP domains d1tkla_ A: Coproporphyrinogen III oxidase                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1tklA00 A:4-328 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh.eeeeeeeee....eeeeeeeeeeeeeeehhhhhh.hhhhh..................eeeeeeeeeeeeee......eeeeeeeeeeee.....eeeeeeeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhheehhhhee....eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..eee..........hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                    Transcript 1
                 1tkl A   4 PQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILMSLPEHASWLYNHHPAPGSREAKLLEVTTKPREWVK 328
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323     


Chain B from PDB  Type:PROTEIN  Length:325
 aligned with HEM6_YEAST | P11353 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:325
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323     
           HEM6_YEAST     4 PQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILMSLPEHASWLYNHHPAPGSREAKLLEVTTKPREWVK 328
               SCOP domains d1tklb_ B: Coproporphyrinogen III oxidase                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1tklB00 B:4-328 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ----------Coprogen_oxidas-1tklB01 B:14-327                                                                                                                                                                                                                                                                                          - Pfam domains (1)
           Pfam domains (2) ----------Coprogen_oxidas-1tklB02 B:14-327                                                                                                                                                                                                                                                                                          - Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhh......eeeeeee....eeeeeeeee....eeeeeeeeeeeeeeehhhhhhhh......................eeeeeeeeeeeeee......eeeeeeeeeeeee...eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhheehhhhee....eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..eee..........hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:4-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                    Transcript 1
                 1tkl B   4 PQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILMSLPEHASWLYNHHPAPGSREAKLLEVTTKPREWVK 328
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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:50 - Gly A:51   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        HEM6_YEAST | P11353: 1tk1 1tlb 1txn

(-) Related Entries Specified in the PDB File

1tk1 1tlb