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(-) Description

Title :  CRYSTAL STRUCTURE OF FERROCHELATASE WITH CADMIUM BOUND AT ACTIVE SITE
 
Authors :  D. Lecerof, M. N. Fodje, R. A. Leon, U. Olsson, A. Hansson, E. Sigfridsson, U. Ryde, M. Hansson, S. Al-Karadaghi
Date :  14 Oct 02  (Deposition) - 27 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Pi-Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Lecerof, M. N. Fodje, R. A. Leon, U. Olsson, A. Hansson, E. Sigfridsson, U. Ryde, M. Hansson, S. Al-Karadaghi
Metal Binding To Bacillus Subtilis Ferrochelatase And Interaction Between Metal Sites
J. Biol. Inorg. Chem. V. 8 452 2003
PubMed-ID: 12761666
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FERROCHELATASE
    Chains: A
    EC Number: 4.99.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2CL2Ligand/IonCHLORIDE ION
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:13 , HIS A:183 , SER A:222 , GLU A:264 , HOH A:982 , HOH A:1052BINDING SITE FOR RESIDUE CD A 910
2AC2SOFTWAREHIS A:262 , HOH A:924 , HOH A:960 , HOH A:962 , HOH A:1264BINDING SITE FOR RESIDUE CD A 911
3AC3SOFTWAREGLU A:145 , LYS A:307BINDING SITE FOR RESIDUE CL A 912
4AC4SOFTWAREARG A:33 , PHE A:117 , SER A:146 , GLN A:199BINDING SITE FOR RESIDUE CL A 913
5AC5SOFTWAREHOH A:1266 , HOH A:1267 , HOH A:1268 , HOH A:1269 , HOH A:1270 , HOH A:1271BINDING SITE FOR RESIDUE MG A 900
6AC6SOFTWAREHOH A:1272 , HOH A:1273 , HOH A:1274 , HOH A:1275 , HOH A:1276 , HOH A:1277BINDING SITE FOR RESIDUE MG A 901
7AC7SOFTWAREGLU A:20 , HOH A:1278 , HOH A:1279 , HOH A:1280 , HOH A:1281 , HOH A:1282BINDING SITE FOR RESIDUE MG A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N0I)

(-) 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 1N0I)

(-) 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 1N0I)

(-) 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:309
 aligned with HEMH_BACSU | P32396 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
           HEMH_BACSU     2 SRKKMGLLVMAYGTPYKEEDIERYYTHIRRGRKPEPEMLQDLKDRYEAIGGISPLAQITEQQAHNLEQHLNEIQDEITFKAYIGLKHIEPFIEDAVAEMHKDGITEAVSIVLAPHFSTFSVQSYNKRAKEEAEKLGGLTITSVESWYDEPKFVTYWVDRVKETYASMPEDERENAMLIVSAHSLPEKIKEFGDPYPDQLHESAKLIAEGAGVSEYAVGWQSEGNTPDPWLGPDVQDLTRDLFEQKGYQAFVYVPVGFVADHLEVLYDNDYECKVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLGR 310
               SCOP domains d1n0ia_ A: Ferrochelatase                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1n0iA01 A:3-147,A:290-310  [code=3.40.50.1400, no name defined]                                                                                  1n0iA02 A:148-289  [code=3.40.50.1400, no name defined]                                                                                       1n0iA01               CATH domains
               Pfam domains ---Ferrochelatase-1n0iA01 A:5-308                                                                                                                                                                                                                                                                                  -- Pfam domains
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhh..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
                 1n0i A   2 SRKKMGLLVMAYGTPYKEEDIERYYTHIRRGRKPEPEMLQDLKDRYEAIGGISPLAQITEQQAHNLEQHLNEIQDEITFKAYIGLKHIEPFIEDAVAEMHKDGITEAVSIVLAPHFSTFSVQSYNKRAKEEAEKLGGLTITSVESWYDEPKFVTYWVDRVKETYASMPEDERENAMLIVSAHSLPEKIKEFGDPYPDQLHESAKLIAEGAGVSEYAVGWQSEGNTPDPWLGPDVQDLTRDLFEQKGYQAFVYVPVGFVADHLEVLYDNDYECKVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLGR 310
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   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 2ac2 2ac4 2h1v 2h1w 2hk6 2q2n 2q2o 2q3j 3goq 3m4z

(-) Related Entries Specified in the PDB File

1c1h SAME ENZYME WITH N-METHYLMESOPORPHYRIN (SUBSTRATE ANALOG) BOUND AT ACTIVE SITE
1c9e SAME ENZYME WITH COPPER(II) N- METHYLMESOPORPHYRIN (PRODUCT ANALOG) BOUND AT THE ACTIVE SITE
1doz APO ENZYME
1ld3 SAME ENZYME WITH ZINC (SUBSTRATE) BOUND AT ACTIVE SITE