Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS SUBTILIS FERROCHELATASE IN COMPLEX WITH N-METHYL MESOPORPHYRIN
 
Authors :  D. Lecerof, M. Fodje, A. Hansson, M. Hansson, S. Al-Karadaghi
Date :  22 Jul 99  (Deposition) - 17 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Alpha/Beta Fold, Ferrochelatase, Heme Synthesis, Porphyrin Metallation, Pi-Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Lecerof, M. Fodje, A. Hansson, M. Hansson, S. Al-Karadaghi
Structural And Mechanistic Basis Of Porphyrin Metallation By Ferrochelatase.
J. Mol. Biol. V. 297 221 2000
PubMed-ID: 10704318  |  Reference-DOI: 10.1006/JMBI.2000.3569
(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 Plasmid: PLUGT7-H
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: 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
1MG1Ligand/IonMAGNESIUM ION
2MMP1Ligand/IonN-METHYLMESOPORPHYRIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:901 , HOH A:902 , HOH A:903 , HOH A:904 , HOH A:905 , HOH A:906BINDING SITE FOR RESIDUE MG A 900
2AC2SOFTWARETYR A:13 , TYR A:25 , ILE A:29 , ARG A:30 , ARG A:31 , ARG A:33 , LYS A:87 , PHE A:120 , SER A:121 , HIS A:183 , LYS A:188 , SER A:222 , THR A:226 , LEU A:263 , GLU A:264 , HOH A:441 , HOH A:507 , HOH A:597 , HOH A:646 , HOH A:712BINDING SITE FOR RESIDUE MMP A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C1H)

(-) 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 1C1H)

(-) 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 1C1H)

(-) 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 d1c1ha_ A: Ferrochelatase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1c1hA01 A:5-147,A:290-310  [code=3.40.50.1400, no name defined]                                                                                1c1hA02 A:148-289  [code=3.40.50.1400, no name defined]                                                                                       1c1hA01               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeee...hhhhhhh.hhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhh..eeeee.......hhhhhh...hhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------FERROCHELATASE     ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c1h A   5 KMGLLVMAYGTPYKEEDIERYYTHIRRGRKPEPEMLQDLKDRYEAIGGISPLAQITEQQAHNLEQHLNEIQDEITFKAYIGLKHIEPFIEDAVAEMHKDGITEAVSIVLAPHFSTFSVQSYNKRAKEEAEKLGGLTITSVESWYDEPKFVTYWVDRVKETYASMPEDERENAMLIVSAHSLPEKIKEFGDPYPDQLHESAKLIAEGAGVSEYAVGWQSEGNTPDPWLGPDVQDLTRDLFEQKGYQAFVYVPVGFVADHLEVLYDNDYECKVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLGR 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  (0, 0)

(no "Pfam Domain" information available for 1C1H)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:90 - Pro A:91   [ RasMol ]  
    Gly A:232 - Pro A:233   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1c1h
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HEMH_BACSU | P32396
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.99.1.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  HEMH_BACSU | P32396
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HEMH_BACSU | P32396: 1ak1 1c9e 1doz 1fji 1ld3 1n0i 2ac2 2ac4 2h1v 2h1w 2hk6 2q2n 2q2o 2q3j 3goq 3m4z

(-) Related Entries Specified in the PDB File

1ak1 BACILLUS SUBTILIS FERROCHELATSE