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(-) Description

Title :  LEISHMANIA MAJOR COPROPORPHYRINOGEN III OXIDASE WITH BOUND LIGAND
 
Authors :  I. Le Trong, E. A. Merritt, Structural Genomics Of Pathogenic Pro Consortium (Sgpp)
Date :  22 Jul 08  (Deposition) - 09 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fragment Cocktail, 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, E. T. Larson, S. Shibata, Z. Zhang, L. Anderson, J. Ross, W. Deng, C. L. M. J. Verlinde, F. S. Buckner, W. C. Van Voorhis, W. G. J. Hol, E. Fan
Leishmania Major Coproporphyrinogen Iii Oxidase With Bound Ligand
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: PET14B, BG1861
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LMAJ006828, LMJF06.1270
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: 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  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2FIC2Ligand/Ion5-FLUOROINDOLE-2-CARBOXYLIC ACID
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:107 , ARG A:181 , TYR A:241 , ASN A:245 , SER A:268 , HOH A:347BINDING SITE FOR RESIDUE ACT A 302
2AC2SOFTWAREHIS B:107 , ARG B:181 , TYR B:241 , ASN B:245 , SER B:268 , HOH B:337BINDING SITE FOR RESIDUE ACT B 302
3AC3SOFTWAREPRO B:122 , TRP B:124 , ASN B:192 , HOH B:568BINDING SITE FOR RESIDUE ACT B 303
4AC4SOFTWARESER A:93 , HIS A:107 , ASN A:109 , ARG A:111 , GLY A:251 , HOH A:504BINDING SITE FOR RESIDUE FIC A 303
5AC5SOFTWARESER B:93 , HIS B:107 , ASN B:109 , ARG B:111 , GLY B:251 , HOH B:546 , HOH B:566BINDING SITE FOR RESIDUE FIC B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 3DWS)

(-) 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 d3dwsa_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3dwsA00 A:0-301 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeeee....eeeeeeeeeeeeee....hhhhhh......eeeeeeeeeeeee......eeeeeeeeeeee......eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee..........hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dws 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 d3dwsb_ B: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3dwsB00 B:-2-301 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeee....eeeeeeeeeeeeee..hhhhh.........eeeeeeeeeeeee......eeeeeeeeeeee......eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee..........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dws 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  (0, 0)

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

(-) 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 2qt8 3dwr

(-) Related Entries Specified in the PDB File

1vju 2qt8 3dwr