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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE FERROCHELATASE
 
Authors :  T. Karlberg, D. Lecerof, M. Gora, G. Silvegren, R. Labbe-Bois, M. Hansson, S. Al-Karadaghi
Date :  04 Apr 02  (Deposition) - 20 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Pi-Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Karlberg, D. Lecerof, M. Gora, G. Silvegren, R. Labbe-Bois, M. Hansson, S. Al-Karadaghi
Metal Binding To Saccharomyces Cerevisiae Ferrochelatase
Biochemistry V. 41 13499 2002
PubMed-ID: 12427010  |  Reference-DOI: 10.1021/BI0260785
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FERROCHELATASE
    Chains: A, B
    EC Number: 4.99.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PROTOHEME FERROLYASE
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LBQ)

(-) Sites  (0, 0)

(no "Site" information available for 1LBQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:139 -Pro A:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERROCHELATASEPS00534 Ferrochelatase signature.HEMH_YEAST230-250
 		  2A:230-250
B:230-250

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YOR176W1YOR176W.1XV:662402-6635831182HEMH_YEAST1-3933932A:36-391
B:38-391		356
354

(-) 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:356
 aligned with HEMH_YEAST | P16622 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:356
                                    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       315       325       335       345       355       365       375       385      
           HEMH_YEAST    36 RSPTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHE 391
               SCOP domains d1lbqa_ A: Ferrochelatase                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1lbqA01 A:36-199,A:339-391  [code=3.40.50.1400, no name defined]                                                                                                    1lbqA02 A:200-338  [code=3.40.50.1400, no name defined]                                                                                    1lbqA01 A:36-199,A:339-391                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhhh....hhhhheeeeeee..hhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhh..eeee.......hhhhhh...........hhh.eee......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FERROCHELATASE       --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:36-391 UniProt: 1-393 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                  Transcript 1
                 1lbq A  36 RSPTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHE 391
                                    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       315       325       335       345       355       365       375       385      


Chain B from PDB  Type:PROTEIN  Length:354
 aligned with HEMH_YEAST | P16622 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:354
                                    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       307       317       327       337       347       357       367       377       387    
           HEMH_YEAST    38 PTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHE 391
               SCOP domains d1lbqb_ B: Ferrochelatase                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1lbqB01 B:38-199,B:339-391  [code=3.40.50.1400, no name defined]                                                                                                  1lbqB02 B:200-338  [code=3.40.50.1400, no name defined]                                                                                    1lbqB01 B:38-199,B:339-391                            CATH domains
           Pfam domains (1) Ferrochelatase-1lbqB01 B:38-357                                                                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains (1)
           Pfam domains (2) Ferrochelatase-1lbqB02 B:38-357                                                                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeee........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh..hhhhhh..eeeeeee..hhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhh.....eeee.......hhhhhh...............eee......hhhhhhhhhhhhhhhhh.......hhhhhhhhh.......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FERROCHELATASE       --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:38-391 UniProt: 1-393 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                Transcript 1
                 1lbq B  38 PTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHE 391
                                    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       307       317       327       337       347       357       367       377       387
   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) (23833)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Chelatase (20)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HEMH_YEAST | P16622)
molecular function
    GO:0004325    ferrochelatase activity    Catalysis of the reaction: protoheme = Fe(2+) + protoporphyrin IX.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
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: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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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    Lys A:139 - Pro A:140   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        HEMH_YEAST | P16622: 1l8x

(-) Related Entries Specified in the PDB File

1l8x THE CO(II) DERIVATIVE