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(-) Description

Title :  CRYSTAL STRUCTURE OF REDUCED ISDI IN COMPLEX WITH HEME
 
Authors :  G. N. Ukpabi, M. E. P. Murphy
Date :  20 Jan 10  (Deposition) - 09 Mar 10  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimeric Alpha+Beta Barrel, Cytoplasm, Heme, Iron, Metal- Binding, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Reniere, G. N. Ukpabi, S. R. Harry, D. F. Stec, R. Krull, D. W. Wright, B. O. Bachmann, M. E. P. Murphy, E. P. Skaar
The Isdg-Family Of Haem Oxygenases Degrades Haem To A Novel Chromophore
Mol. Microbiol. V. 75 1529 2010
PubMed-ID: 20180905  |  Reference-DOI: 10.1111/J.1365-2958.2010.07076.X

(-) Compounds

Molecule 1 - HEME-DEGRADING MONOOXYGENASE ISDI
    Chains: A, B
    EC Number: 1.14.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ISDI
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158879
    Strain: N315
    Synonym: ISDI, IRON-REGULATED SURFACE DETERMINANT ISDI, IRON-RESPONSIVE SURFACE DETERMINANT ISDI, HEME OXYGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:6 , ARG A:21 , PHE A:22 , ARG A:25 , GLN A:26 , GLY A:27 , ILE A:28 , THR A:55 , TRP A:66 , ALA A:75 , HIS A:76 , VAL A:79 , ASN A:95 , VAL A:97 , HOH A:144BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWAREASN B:6 , ARG B:21 , PHE B:22 , ARG B:25 , GLN B:26 , GLY B:27 , ILE B:28 , THR B:55 , TRP B:66 , ALA B:75 , HIS B:76 , VAL B:79 , ASN B:95 , VAL B:97 , HOH B:120 , HOH B:147 , HOH B:160 , HOH B:161 , HOH B:207BINDING SITE FOR RESIDUE HEM B 200
3AC3SOFTWAREHOH B:601 , HOH B:602 , HOH B:603 , HOH B:604 , HOH B:605 , HOH B:606BINDING SITE FOR RESIDUE MG B 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LGM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LGM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LGM)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABMPS51725 ABM domain profile.HDOX2_STAAN2-93
 		  2A:2-93
B:2-93

(-) Exons   (0, 0)

(no "Exon" information available for 3LGM)

(-) 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:110
 aligned with HDOX2_STAAN | Q7A827 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:110
                              1                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108
          HDOX2_STAAN     - --MFMAENRLQLQKGSAEETIERFYNRQGIETIEGFQQMFVTKTLNTEDTDEVKILTIWESEDSFNNWLNSDVFKEAHKNVRLKSDDDGQQSPILSNKVFKYDIGYHYQK 108
               SCOP domains d3lgma_ A: Hypothetical protein PG130 (SAV0165)                                                                SCOP domains
               CATH domains 3lgmA00 A:-1-108  [code=3.30.70.900, no name defined]                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhh.....hhhhh..eeeeeeeeee....eeeeeeeeee.hhhhhhhhhhhhhhhhhhh..............eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ABM  PDB: A:2-93 UniProt: 2-93                                                              --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3lgm A  -1 AHMFMAENRLQLQKGSAEETIERFYNRQGIETIEGFQQMFVTKTLNTEDTDEVKILTIWESEDSFNNWLNSDVFKEAHKNVRLKSDDDGQQSPILSNKVFKYDIGYHYQK 108
                                     8        18        28        38        48        58        68        78        88        98       108


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with HDOX2_STAAN | Q7A827 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:110
                              1                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108
          HDOX2_STAAN     - --MFMAENRLQLQKGSAEETIERFYNRQGIETIEGFQQMFVTKTLNTEDTDEVKILTIWESEDSFNNWLNSDVFKEAHKNVRLKSDDDGQQSPILSNKVFKYDIGYHYQK 108
               SCOP domains d3lgmb_ B: Hypothetical protein PG130 (SAV0165)                                                                SCOP domains
               CATH domains 3lgmB00 B:-1-108  [code=3.30.70.900, no name defined]                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...hhhhhhhh.....hhhhh..eeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhh..............eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ABM  PDB: B:2-93 UniProt: 2-93                                                              --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3lgm B  -1 AHMFMAENRLQLQKGSAEETIERFYNRQGIETIEGFQQMFVTKTLNTEDTDEVKILTIWESEDSFNNWLNSDVFKEAHKNVRLKSDDDGQQSPILSNKVFKYDIGYHYQK 108
                                     8        18        28        38        48        58        68        78        88        98       108
   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) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LGM)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HDOX2_STAAN | Q7A827)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0004392    heme oxygenase (decyclizing) activity    Catalysis of the reaction: heme + 3 donor-H2 + 3 O2 = biliverdin + Fe2+ + CO + 3 acceptor + 3 H2O.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
biological process
    GO:0042167    heme catabolic process    The chemical reactions and pathways resulting in the breakdown of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0033212    iron assimilation    A process in which iron is solubilized and transported into a cell.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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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  1.14.99.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        HDOX2_STAAN | Q7A827: 2zdp 3lgn 3qgp 4fnh 4fni

(-) Related Entries Specified in the PDB File

3lgn ISDI IN COMPLEX WITH HEME