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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIS183ALA VARIANT OF BACILLUS SUBTILIS FERROCHELATASE IN COMPLEX WITH N-METHYL MESOPORPHYRIN
 
Authors :  T. Karlberg, O. H. Thorvaldsen, S. Al-Karadaghi
Date :  30 May 07  (Deposition) - 22 Apr 08  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold; Pi-Helix; N-Methyl Mesoporphyrin Ix; N-Memp, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Karlberg, M. D. Hansson, R. K. Yengo, R. Johansson, O. H. Thorvaldsen, G. C. Ferreira, M. Hansson, S. Al-Karadaghi
Porphyrin Binding And Distortion And Substrate Specificity In The Ferrochelatase Reaction: The Role Of Active Site Residues
J. Mol. Biol. V. 378 1074 2008
PubMed-ID: 18423489  |  Reference-DOI: 10.1016/J.JMB.2008.03.040

(-) Compounds

Molecule 1 - FERROCHELATASE
    Chains: A
    EC Number: 4.99.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PH183A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HEMH, HEMF
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PROTOHEME FERRO-LYASE;
HEME SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1H021Ligand/IonN-METHYL PROTOPORPHYRIN IX 2,4-DISULFONIC ACID
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1001 , HOH A:1002 , HOH A:1003 , HOH A:1004 , HOH A:1005 , HOH A:1006BINDING SITE FOR RESIDUE MG A 1000
2AC2SOFTWARETYR A:13 , TYR A:26 , ILE A:29 , ARG A:31 , PHE A:120 , SER A:121 , ALA A:183 , SER A:222 , GLY A:224 , ASN A:225 , THR A:226 , TRP A:230 , GLU A:264 , HOH A:1123BINDING SITE FOR RESIDUE H02 A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q3J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:90 -Pro A:91
2Gly A:232 -Pro A:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q3J)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERROCHELATASEPS00534 Ferrochelatase signature.HEMH_BACSU178-196  1A:178-196

(-) Exons   (0, 0)

(no "Exon" information available for 2Q3J)

(-) 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:306
 aligned with HEMH_BACSU | P32396 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:306
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304      
           HEMH_BACSU     5 KMGLLVMAYGTPYKEEDIERYYTHIRRGRKPEPEMLQDLKDRYEAIGGISPLAQITEQQAHNLEQHLNEIQDEITFKAYIGLKHIEPFIEDAVAEMHKDGITEAVSIVLAPHFSTFSVQSYNKRAKEEAEKLGGLTITSVESWYDEPKFVTYWVDRVKETYASMPEDERENAMLIVSAHSLPEKIKEFGDPYPDQLHESAKLIAEGAGVSEYAVGWQSEGNTPDPWLGPDVQDLTRDLFEQKGYQAFVYVPVGFVADHLEVLYDNDYECKVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLGR 310
               SCOP domains d2q3ja_ A: Ferrochelatase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2q3jA01 A:5-147,A:290-310  [code=3.40.50.1400, no name defined]                                                                                2q3jA02 A:148-289  [code=3.40.50.1400, no name defined]                                                                                       2q3jA01               CATH domains
               Pfam domains Ferrochelatase-2q3jA01 A:5-308                                                                                                                                                                                                                                                                                  -- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeee..hhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhh..eeeee.......hhhhhh...hhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------FERROCHELATASE     ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q3j A   5 KMGLLVMAYGTPYKEEDIERYYTHIRRGRKPEPEMLQDLKDRYEAIGGISPLAQITEQQAHNLEQHLNEIQDEITFKAYIGLKHIEPFIEDAVAEMHKDGITEAVSIVLAPHFSTFSVQSYNKRAKEEAEKLGGLTITSVESWYDEPKFVTYWVDRVKETYASMPEDERENAMLIVSAASLPEKIKEFGDPYPDQLHESAKLIAEGAGVSEYAVGWQSEGNTPDPWLGPDVQDLTRDLFEQKGYQAFVYVPVGFVADHLEVLYDNDYECKVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLGR 310
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HEMH_BACSU | P32396)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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
        HEMH_BACSU | P32396: 1ak1 1c1h 1c9e 1doz 1fji 1ld3 1n0i 2ac2 2ac4 2h1v 2h1w 2hk6 2q2n 2q2o 3goq 3m4z

(-) Related Entries Specified in the PDB File

2q2n 2q2o