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(-) Description

Title :  COPROPORPHYRINOGEN III OXIDASE FROM LEISHMANIA DONOVANI
 
Authors :  E. T. Larson, E. A. Merritt, Medical Structural Genomics Of Pathog Protozoa (Msgpp)
Date :  18 Sep 08  (Deposition) - 14 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heme Metabolism, Medical Structural Genomics Of Pathogenic Protozoa Consortium, Msgpp, Heme Biosynthesis, Oxidoreductase, Porphyrin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. T. Larson, E. A. Merritt, Medical Structural Genomics Of Pathogenic Protozoa Consortium (Msgpp)
Structural Investigation Of A Protozoan Coproporphyrinogen Iii Oxidase
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: BG1861
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: LEISHMANIA DONOVANI
    Organism Taxid: 5661

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:95 , HIS A:107 , ARG A:181 , TYR A:241 , ASN A:245BINDING SITE FOR RESIDUE ACT A 302
2AC2SOFTWAREVAL B:95 , HIS B:107 , ARG B:181 , TYR B:241 , ASN B:245 , HOH B:317BINDING SITE FOR RESIDUE ACT B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EJO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EJO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EJO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EJO)

(-) Exons   (0, 0)

(no "Exon" information available for 3EJO)

(-) 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:292
 aligned with D0VX00_LEIDO | D0VX00 from UniProtKB/TrEMBL  Length:302

    Alignment length:301
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301 
         D0VX00_LEIDO     2 MSLAIEAVKDFLVKLQDDICEALEAEDGQATFMEDKWTREGGGGGRTRVMVNGAVIEKGGVNFSHVYGKGLPGSSTERHPDMTGCNFQAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRYFHQVAQDLCKPFGADVYTRFKVWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYIDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYDWQPEPGTPEARLTEYFLMKRQWV 302
               SCOP domains d3ejoa_ A: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3ejoA00 A:1-301 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeeee....eeeeeeeeeee.....---------.....eeeeeeeeeeeee......eeeeeeeeeeee......eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ejo A   1 MSLAIEAVKDFLVKLQDDICEALEAEDGQATFMEDKWTREGGGGGRTRVMVNGAVIEKGGVNFSHVYGKGL---------DMTGCNFQAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRYFHQVAQDLCKPFGADVYTRFKVWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYIDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYDWQPEPGTPEARLTEYFLMKRQWV 301
                                    10        20        30        40        50        60        70|        -|       90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                                                                                 71        81                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with D0VX00_LEIDO | D0VX00 from UniProtKB/TrEMBL  Length:302

    Alignment length:301
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301 
         D0VX00_LEIDO     2 MSLAIEAVKDFLVKLQDDICEALEAEDGQATFMEDKWTREGGGGGRTRVMVNGAVIEKGGVNFSHVYGKGLPGSSTERHPDMTGCNFQAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRYFHQVAQDLCKPFGADVYTRFKVWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYIDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYDWQPEPGTPEARLTEYFLMKRQWV 302
               SCOP domains d3ejob_ B: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3ejoB00 B:1-301 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeee....eeeeeeeeeeeee...----------....eeeeeeeeeeeee......eeeeeeeeeeee......eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee..........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ejo B   1 MSLAIEAVKDFLVKLQDDICEALEAEDGQATFMEDKWTREGGGGGRTRVMVNGAVIEKGGVNFSHVYGKGL----------MTGCNFQAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRYFHQVAQDLCKPFGADVYTRFKVWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYIDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYDWQPEPGTPEARLTEYFLMKRQWV 301
                                    10        20        30        40        50        60        70|        - |      90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                                                                                 71         82
   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  (0, 0)

(no "Pfam Domain" information available for 3EJO)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (D0VX00_LEIDO | D0VX00)
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.
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.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1vju HOMOLOGOUS ENZYME FROM L. MAJOR
2qt8 HOMOLOGOUS ENZYME FROM L. MAJOR
3dwr HOMOLOGOUS ENZYME FROM L. MAJOR IN COMPLEX WITH CPA
3dws HOMOLOGOUS ENZYME FROM L. MAJOR IN COMPLEX WITH FIC
3e8j HOMOLOGOUS ENZYME FROM L. NAIFFI RELATED ID: LDON006828AAA RELATED DB: TARGETDB