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(-) Description

Title :  COPROPORPHYRINOGEN III OXIDASE FROM LEISHMANIA NAIFFI
 
Authors :  E. T. Larson, E. A. Merritt, Medical Structural Genomics Of Pathog Protozoa (Msgpp)
Date :  19 Aug 08  (Deposition) - 02 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
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 (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: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SIMILAR TO LBRM06_V2.1260
    Organism Scientific: LEISHMANIA NAIFFI
    Organism Taxid: 5678

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL5Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:95 , HIS A:107 , ARG A:181 , TYR A:241 , ASN A:245 , SER A:268 , HOH A:317BINDING SITE FOR RESIDUE ACT A 302
2AC2SOFTWAREPHE A:173 , LYS A:298 , HOH A:367BINDING SITE FOR RESIDUE GOL A 303
3AC3SOFTWARETRP A:167 , GLU A:170 , HOH A:403BINDING SITE FOR RESIDUE GOL A 304
4AC4SOFTWAREVAL A:123 , TRP A:124 , ASN A:192BINDING SITE FOR RESIDUE GOL A 305
5AC5SOFTWAREVAL B:95 , HIS B:107 , ARG B:181 , TYR B:241 , ASN B:245 , HOH B:421BINDING SITE FOR RESIDUE ACT B 302
6AC6SOFTWARETRP B:167 , GLU B:170 , HOH B:413 , HOH B:438BINDING SITE FOR RESIDUE GOL B 303
7AC7SOFTWARELYS B:298BINDING SITE FOR RESIDUE GOL B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E8J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E8J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E8J)

(-) Exons   (0, 0)

(no "Exon" information available for 3E8J)

(-) 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:285
 aligned with D0VWU6_9TRYP | D0VWU6 from UniProtKB/TrEMBL  Length:306

    Alignment length:299
                                    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         
         D0VWU6_9TRYP     8 LPVEAVKEFLLKLQDDICHAIEAEDEQATFMEDKWTREGGGGGRTRVIANGAVIEKGGVNFSHVYGKGLPGSSTERHPDMAGCNYQAMGVSLVIHPKNPHVPTSHANVRLFVAEKEGKEPVWWFGGGFDLTPYYAVEEDCYYFHHVAQELCRPFGADVYERFKAWCDEYFFIPHRNEARGIGGLFFDDLNEWPFEKCFAFMQAVGKGFIDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILMSLPPRARWGYNWHPEPGTPEARLTEYFLTKKQWV 306
               SCOP domains d3e8ja_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3e8jA00 A:3-301 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeee....eeeeeeeeeeee...--------------.eeeeeeeeeeeee......eeeeeeeeeeee......eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee..........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e8j A   3 LPVEAVKEFLLKLQDDICHAIEAEDEQATFMEDKWTREGGGGGRTRVIANGAVIEKGGVNFSHVYGKG--------------CNYQAMGVSLVIHPKNPHVPTSHANVRLFVAEKEGKEPVWWFGGGFDLTPYYAVEEDCYYFHHVAQELCRPFGADVYERFKAWCDEYFFIPHRNEARGIGGLFFDDLNEWPFEKCFAFMQAVGKGFIDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILMSLPPRARWGYNWHPEPGTPEARLTEYFLTKKQWV 301
                                    12        22        32        42        52        62       | -         -  |     92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292         
                                                                                              70             85                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with D0VWU6_9TRYP | D0VWU6 from UniProtKB/TrEMBL  Length:306

    Alignment length:301
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305 
         D0VWU6_9TRYP     6 MSLPVEAVKEFLLKLQDDICHAIEAEDEQATFMEDKWTREGGGGGRTRVIANGAVIEKGGVNFSHVYGKGLPGSSTERHPDMAGCNYQAMGVSLVIHPKNPHVPTSHANVRLFVAEKEGKEPVWWFGGGFDLTPYYAVEEDCYYFHHVAQELCRPFGADVYERFKAWCDEYFFIPHRNEARGIGGLFFDDLNEWPFEKCFAFMQAVGKGFIDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILMSLPPRARWGYNWHPEPGTPEARLTEYFLTKKQWV 306
               SCOP domains d3e8jb_ B: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3e8jB00 B:1-301 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...eeeeeeeee....eeeeeeeeeeeee..-------------...eeeeeeeeeeee......eeeeeeeeeee.--....eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee.............hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e8j B   1 MSLPVEAVKEFLLKLQDDICHAIEAEDEQATFMEDKWTREGGGGGRTRVIANGAVIEKGGVNFSHVYGKG-------------GCNYQAMGVSLVIHPKNPHVPTSHANVRLFVAE--GKEPVWWFGGGFDLTPYYAVEEDCYYFHHVAQELCRPFGADVYERFKAWCDEYFFIPHRNEARGIGGLFFDDLNEWPFEKCFAFMQAVGKGFIDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILMSLPPRARWGYNWHPEPGTPEARLTEYFLTKKQWV 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 
                                                                                                70            84                             116  |                                                                                                                                                                                      
                                                                                                                                                119
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3E8J)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (D0VWU6_9TRYP | D0VWU6)
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

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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 RELATED ID: LNAI006828AAA RELATED DB: TARGETDB