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(-) Description

Title :  COPROPORPHYRINOGEN III OXIDASE FROM LEISHMANIA MAJOR
 
Authors :  E. A. Merritt, Structural Genomics Of Pathogenic Protozoa Conso (Sgpp)
Date :  01 Aug 07  (Deposition) - 04 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heme Metabolism, Structural Genomics, Structural Genomics Of Pathogenic Protozoa Consortium, Sgpp, Heme Biosynthesis, Oxidoreductase, Porphyrin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Merritt, I. Le Trong
Coproporphyrinogen Iii Oxidase From Leishmania Major.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COPROPORPHYRINOGEN III OXIDASE
    Chains: A, B
    EC Number: 1.3.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LMJF06.1270, LMAJ006828
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: MHOM/IL/81/FRIEDLIN
    Synonym: COPROPORPHYRINOGENASE, COPROGEN OXIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2QT8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QT8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QT8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QT8)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPROGEN_OXIDASEPS01021 Coproporphyrinogen III oxidase signature.HEM6_LEIMA165-189
 		  2A:165-189
B:165-189

(-) Exons   (0, 0)

(no "Exon" information available for 2QT8)

(-) 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:302
 aligned with HEM6_LEIMA | P84155 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:302
                             1                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299  
           HEM6_LEIMA     - -MSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVMVDGAVIEKGGVNFSHVYGKGLPMSSTERHPDIAGCNFEAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYMDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
               SCOP domains d2qt8a_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2qt8A00 A:0-301 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeee....eeeeeeeeeeeeee..hhhhhh........eeeeeeeeeeeee......eeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee..........hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qt8 A   0 HmSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVmVDGAVIEKGGVNFSHVYGKGLPmSSTERHPDIAGCNFEAmGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYmDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
                             |       9        19        29        39        49|       59        69   |    79        89|       99       109       119       129       139       149       159       169       179       189       199       209 |     219       229       239       249       259       269       279       289       299  
                             |                                               50-MSE                 73-MSE           90-MSE                                                                                                                  211-MSE                                                                                      
                             1-MSE                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:304
 aligned with HEM6_LEIMA | P84155 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:304
                               1                                                                                                                                                                                                                                                                                                            
                               |     7        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    
           HEM6_LEIMA     - ---MSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVMVDGAVIEKGGVNFSHVYGKGLPMSSTERHPDIAGCNFEAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYMDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
               SCOP domains d2qt8b_ B: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2qt8B00 B:-2-301 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) --------Coprogen_oxidas-2qt8B01 B:6-301                                                                                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) --------Coprogen_oxidas-2qt8B02 B:6-301                                                                                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeee....eeeeeeeeeeeeee..hhhhh.........eeeeeeeeeeeee......eeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee..........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qt8 B  -2 HHHmSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVmVDGAVIEKGGVNFSHVYGKGLPmSSTERHPDIAGCNFEAmGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYmDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
                               |     7        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    
                               1-MSE                                           50-MSE                 73-MSE           90-MSE                                                                                                                  211-MSE
   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  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HEM6_LEIMA | P84155)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HEM6_LEIMA | P84155: 1vju 3dwr 3dws

(-) Related Entries Specified in the PDB File

1vju UNCHARACTERIZED PROTEIN FROM LEISHMANIA MAJOR LMAJ006828