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(-) Description

Title :  CRYSTAL STRUCTURES OF THE NO-AND CO-BOUND HEME OXYGENASE FROM NEISSERIA MENINGITIDIS: IMPLICATIONS FOR OXYGEN ACTIVATION
 
Authors :  J. Friedman, L. Lad, R. Deshmukh, H. Li, A. Wilks, T. L. Poulos
Date :  18 Apr 03  (Deposition) - 09 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Heme Oxygenase, Heme Degradation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Friedman, L. Lad, R. Deshmukh, H. Li, A. Wilks, T. L. Poulos
Crystal Structures Of The No- And Co-Bound Heme Oxygenase From Neisseriae Meningitidis. Implications For O2 Activation
J. Biol. Chem. V. 278 34654 2003
PubMed-ID: 12819228  |  Reference-DOI: 10.1074/JBC.M302985200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEME OXYGENASE 1
    Chains: A
    EC Number: 1.14.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PWMZ1651
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HEMO
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 487
    Other Details: HEME-COMPLEXED
    Synonym: HO-1;
HEME OXYGENASE (DECYCLIZING) 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:16 , HIS A:23 , ASP A:27 , MET A:31 , TYR A:112 , CYS A:113 , GLY A:116 , SER A:117 , LEU A:119 , GLY A:120 , PHE A:123 , LEU A:124 , PHE A:181 , TYR A:184 , HOH A:332 , HOH A:355BINDING SITE FOR RESIDUE HEM A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P3T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P3T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P3T)

(-) Exons   (0, 0)

(no "Exon" information available for 1P3T)

(-) 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:199
 aligned with Q9RGD9_NEIME | Q9RGD9 from UniProtKB/TrEMBL  Length:230

    Alignment length:199
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         
         Q9RGD9_NEIME    29 ALTFAKRLKADTTAVHDSVDNLVMSVQPFVSKENYIKFLKLQSVFHKAVDHIYKDAELNKAIPELEYMARYDAVTQDLKDLGEEPYKFDKELPYEAGNKAIGWLYCAEGSNLGAAFLFKHAQKLDYNGEHGARHLAPHPDGRGKHWRAFVEHLNALNLTPEAEAEAIQGAREAFAFYKVVLRETFGLAADAEAPEGMMP 227
               SCOP domains d1p3ta_ A: Heme oxygenase HemO (PigA)                                                                                                                                                                   SCOP domains
               CATH domains 1p3tA00 A:8-206 Heme Oxygenase; Chain A                                                                                                                                                                 CATH domains
               Pfam domains -Heme_oxygenase-1p3tA01 A:9-190                                                                                                                                                        ---------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p3t A   8 ALTFAKRLKADTTAVHDSVDNLVMSVQPFVSKENYIKFLKLQSVFHKAVDHIYKDAELNKAIPELEYMARYDAVTQDLKDLGEEPYKFDKELPYEAGNKAIGWLYCAEGSNLGAAFLFKHAQKLDYNGEHGARHLAPHPDGRGKHWRAFVEHLNALNLTPEAEAEAIQGAREAFAFYKVVLRETFGLAADAEAPEGMMP 206
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HO (49)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9RGD9_NEIME | Q9RGD9)
molecular function
    GO:0004392    heme oxygenase (decyclizing) activity    Catalysis of the reaction: heme + 3 donor-H2 + 3 O2 = biliverdin + Fe2+ + CO + 3 acceptor + 3 H2O.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006788    heme oxidation    The chemical reactions and pathways resulting in the loss of electrons from one or more atoms in heme.
    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.

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 Related Entries

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        Q9RGD9_NEIME | Q9RGD9: 1j77 1p3u 1p3v

(-) Related Entries Specified in the PDB File

1oyk 1oyl 1oze 1ozl 1ozr 1ozw 1p3u 1p3v