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(-) Description

Title :  CRYSTAL STRUCTURE OF H183C BACILLUS SUBTILIS FERROCHELATASE IN COMPLEX WITH DEUTEROPORPHYRIN IX 2,4-DISULFONIC ACID DIHYDROCHLORIDE
 
Authors :  T. Karlberg, O. H. Thorvaldsen, S. Al-Karadaghi
Date :  29 May 07  (Deposition) - 17 Jun 08  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold; Pi-Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Karlberg, M. D. Hansson, R. K. Yengo, R. Johansson, H. O. 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
    Expression System Plasmid: PH183A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    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
1H011Ligand/IonPROTOPORPHYRIN IX 2,4-DISULFONIC ACID
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:9002 , HOH A:9003 , HOH A:9004 , HOH A:9005 , HOH A:9006 , HOH A:9007BINDING SITE FOR RESIDUE MG A 1000
2AC2SOFTWARETYR A:13 , TYR A:26 , ILE A:29 , ARG A:30 , ARG A:31 , ARG A:33 , PHE A:120 , CYS A:183 , SER A:184 , LEU A:185 , GLN A:199 , GLY A:224 , ASN A:225 , THR A:226 , PRO A:227 , TRP A:230 , HOH A:9026 , HOH A:9031 , HOH A:9092BINDING SITE FOR RESIDUE H01 A 9001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q2O)

(-) 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 2Q2O)

(-) 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 2Q2O)

(-) 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:307
 aligned with HEMH_BACSU | P32396 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
           HEMH_BACSU     4 KKMGLLVMAYGTPYKEEDIERYYTHIRRGRKPEPEMLQDLKDRYEAIGGISPLAQITEQQAHNLEQHLNEIQDEITFKAYIGLKHIEPFIEDAVAEMHKDGITEAVSIVLAPHFSTFSVQSYNKRAKEEAEKLGGLTITSVESWYDEPKFVTYWVDRVKETYASMPEDERENAMLIVSAHSLPEKIKEFGDPYPDQLHESAKLIAEGAGVSEYAVGWQSEGNTPDPWLGPDVQDLTRDLFEQKGYQAFVYVPVGFVADHLEVLYDNDYECKVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLGR 310
               SCOP domains d2q2oa_ A: Ferrochelatase                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2q2oA01 A:4-147,A:290-310  [code=3.40.50.1400, no name defined]                                                                                 2q2oA02 A:148-289  [code=3.40.50.1400, no name defined]                                                                                       2q2oA01               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhh.hhhhhhhhhhhhhhhhh....eeeeee............hhhhhhhhhhhhh...eeeee.......hhhhhh...hhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FERROCHELATASE     ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2o A   4 KKMGLLVMAYGTPYKEEDIERYYTHIRRGRKPEPEMLQDLKDRYEAIGGISPLAQITEQQAHNLEQHLNEIQDEITFKAYIGLKHIEPFIEDAVAEMHKDGITEAVSIVLAPHFSTFSVQSYNKRAKEEAEKLGGLTITSVESWYDEPKFVTYWVDRVKETYASMPEDERENAMLIVSACSLPEKIKEFGDPYPDQLHESAKLIAEGAGVSEYAVGWQSEGNTPDPWLGPDVQDLTRDLFEQKGYQAFVYVPVGFVADHLEVLYDNDYECKVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLGR 310
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303
   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  (0, 0)

(no "Pfam Domain" information available for 2Q2O)

(-) 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 2q3j 3goq 3m4z

(-) Related Entries Specified in the PDB File

2q2n 2q3j