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(-) Description

Title :  COPROPORPHYRINOGEN III OXIDASE (HEMN) FROM ESCHERICHIA COLI IS A RADICAL SAM ENZYME.
 
Authors :  G. Layer, J. Moser, D. W. Heinz, D. Jahn, W. -D. Schubert
Date :  13 Aug 03  (Deposition) - 04 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A
Keywords :  Heme Biosynthesis, Decarboxylase, Radical Sam Enzyme, 4Fe- 4S Cluster, S-Adenosyl-L-Methionine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Layer, J. Moser, D. W. Heinz, D. Jahn, W. -D. Schubert
Crystal Structure Of Coproporphyrinogen Iii Oxidase Reveals Cofactor Geometry Of Radical Sam Enzymes
Embo J. V. 22 6214 2003
PubMed-ID: 14633981  |  Reference-DOI: 10.1093/EMBOJ/CDG598

(-) Compounds

Molecule 1 - OXYGEN-INDEPENDENT COPROPORPHYRINOGEN III OXIDASE
    Chains: A
    EC Number: 1.3.-.-
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: COPROPORPHYRINOGENASE, COPROGEN OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:68 , CYS A:69 , GLY A:70 , CYS A:71 , GLY A:112 , GLY A:113 , THR A:114 , GLU A:145 , VAL A:146 , ASP A:147 , GLY A:170 , GLN A:172 , ARG A:184 , ASP A:209 , ILE A:211 , PHE A:240 , ASN A:241 , TYR A:242 , ALA A:243 , GLN A:252 , SF4 A:500 , SAM A:502 , HOH A:2179BINDING SITE FOR RESIDUE SAM A 501
2AC2SOFTWARETYR A:56 , HIS A:58 , GLY A:111 , GLY A:112 , GLU A:145 , PHE A:240 , PHE A:310 , GLN A:311 , SER A:327 , ALA A:328 , ILE A:329 , SAM A:501 , HOH A:2342 , HOH A:2391 , HOH A:2392 , HOH A:2393 , HOH A:2394 , HOH A:2396BINDING SITE FOR RESIDUE SAM A 502
3AC3SOFTWARECYS A:62 , CYS A:66 , PHE A:68 , CYS A:69 , LYS A:73 , GLY A:113 , THR A:114 , ARG A:149 , ARG A:184 , SAM A:501BINDING SITE FOR RESIDUE SF4 A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:26 -Pro A:27
2Gly A:112 -Gly A:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OLT)

(-) 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:434
 aligned with HEMN_ECOLI | P32131 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:441
                                    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       333       343       353       363       373       383       393       403       413       423       433       443 
           HEMN_ECOLI     4 QQIDWDLALIQKYNYSGPRYTSYPTALEFSEDFGEQAFLQAVARYPERPLSLYVHIPFCHKLCYFCGCNKIVTRQQHKADQYLDALEQEIVHRAPLFAGRHVSQLHWGGGTPTYLNKAQISRLMKLLRENFQFNADAEISIEVDPREIELDVLDHLRAEGFNRLSMGVQDFNKEVQRLVNREQDEEFIFALLNHAREIGFTSTNIDLIYGLPKQTPESFAFTLKRVAELNPDRLSVFNYAHLPTIFAAQRKIKDADLPSPQQKLDILQETIAFLTQSGYQFIGMDHFARPDDELAVAQREGVLHRNFQGYTTQGDTDLLGMGVSAISMIGDCYAQNQKELKQYYQQVDEQGNALWRGIALTRDDCIRRDVIKSLICNFRLDYAPIEKQWDLHFADYFAEDLKLLAPLAKDGLVDVDEKGIQVTAKGRLLIRNICMCFDTYL 444
               SCOP domains d1olta_ A:  O      xygen-independent coproporphyrinogen III oxidase HemN                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------Radical_SAM-1oltA02 A:56-229                                                                                                                                                  -------------------------------------------------------------------------------------------------------------------------------------HemN_C-1oltA01 A:363-431                                             ------------- Pfam domains
         Sec.struct. author ..........-..------.....hhhhh....hhhhhhhhhh......eeeeeee.ee...........ee...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee......hhhhhhhhhh...eeeeeee..hhhhhhhhh...hhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeee..eee...hhhhhhhhhh..ee....ee.....eeeee....eeee..eeeee..hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhheeehhhhhhhh..hhhhhhhhhhhhhhhhhhh..eee...eeee...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1olt A   4 QQIDWDLALI-KY------YTSYPTALEFSEDFGEQAFLQAVARYPERPLSLYVHIPFCHKLCYFCGCNKIVTRQQHKADQYLDALEQEIVHRAPLFAGRHVSQLHWGGGTPTYLNKAQISRLMKLLRENFQFNADAEISIEVDPREIELDVLDHLRAEGFNRLSMGVQDFNKEVQRLVNREQDEEFIFALLNHAREIGFTSTNIDLIYGLPKQTPESFAFTLKRVAELNPDRLSVFNYAHLPTIFAAQRKIKDADLPSPQQKLDILQETIAFLTQSGYQFIGMDHFARPDDELAVAQREGVLHRNFQGYTTQGDTDLLGMGVSAISMIGDCYAQNQKELKQYYQQVDEQGNALWRGIALTRDDCIRRDVIKSLICNFRLDYSPIEQQWDLLFADYFAEDLKLLAPLAKDGLVDVDEKGIQVTAKGRLLIRNICMCFDTYL 444
                                    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       333       343       353       363       373       383       393       403       413       423       433       443 
                                    13 ||     23                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                      15|                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                       16
   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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OLT)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: no clan defined [family: Radical_SAM] (7)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HEMN_ECOLI | P32131)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0051989    coproporphyrinogen dehydrogenase activity    Catalysis of the reaction: coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    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.

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