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(-) Description

Title :  CRYSTAL STRUCTURE OF HEME OXYGENASE-1 FROM CYANOBACTERIUM SYNECHOCYSTIS SP. PCC6803 IN COMPLEX WITH HEME
 
Authors :  M. Sugishima, C. T. Migita, X. Zhang, T. Yoshida, K. Fukuyama
Date :  21 May 04  (Deposition) - 21 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sugishima, C. T. Migita, X. Zhang, T. Yoshida, K. Fukuyama
Crystal Structure Of Heme Oxygenase-1 From Cyanobacterium Synechocystis Sp. Pcc 6803 In Complex With Heme
Eur. J. Biochem. V. 271 4517 2004
PubMed-ID: 15560792  |  Reference-DOI: 10.1111/J.1432-1033.2004.04411.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEME OXYGENASE 1
    ChainsA, B, C, D
    EC Number1.14.99.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPMW172
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificSYNECHOCYSTIS SP.
    Organism Taxid1148
    StrainPCC 6803

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IPA8Ligand/IonISOPROPYL ALCOHOL
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IPA2Ligand/IonISOPROPYL ALCOHOL
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IPA2Ligand/IonISOPROPYL ALCOHOL
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IPA2Ligand/IonISOPROPYL ALCOHOL
4PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IPA2Ligand/IonISOPROPYL ALCOHOL
4PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:165 , LYS A:168 , LYS D:165 , LYS D:168 , ARG D:172BINDING SITE FOR RESIDUE PO4 A 241
02AC2SOFTWARELYS B:165 , LYS B:168 , ARG B:172 , LYS C:165 , LYS C:168 , ARG C:172BINDING SITE FOR RESIDUE PO4 B 241
03AC3SOFTWARELYS B:14BINDING SITE FOR RESIDUE CL B 242
04AC4SOFTWAREARG C:10BINDING SITE FOR RESIDUE CL C 241
05AC5SOFTWAREARG A:108 , ASP A:194BINDING SITE FOR RESIDUE CL A 243
06AC6SOFTWAREARG A:10 , HIS A:17 , ALA A:20 , LEU A:30 , TYR A:125 , THR A:126 , GLY A:130 , SER A:133 , ILE A:137 , LEU A:138 , LYS A:168 , ARG A:172 , PHE A:203 , HOH A:1006 , LYS D:165BINDING SITE FOR RESIDUE HEM A 300
07AC7SOFTWAREARG B:10 , HIS B:17 , ALA B:20 , VAL B:26 , LEU B:30 , TYR B:125 , THR B:126 , GLY B:130 , SER B:133 , GLY B:134 , LEU B:138 , PHE B:196 , ASN B:199 , HOH B:1007 , HOH B:1051 , LYS C:165BINDING SITE FOR RESIDUE HEM B 300
08AC8SOFTWARELYS B:165 , ARG C:10 , HIS C:17 , ALA C:20 , VAL C:26 , TYR C:125 , THR C:126 , GLY C:130 , SER C:133 , ILE C:137 , LEU C:138 , PHE C:196 , ASN C:199 , HOH C:1008 , HOH C:1011 , HOH C:1012BINDING SITE FOR RESIDUE HEM C 300
09AC9SOFTWARELYS A:165 , ARG D:10 , HIS D:17 , ALA D:20 , VAL D:26 , LEU D:30 , TYR D:125 , THR D:126 , ARG D:127 , GLY D:130 , SER D:133 , ILE D:137 , ARG D:172 , PHE D:196 , ASN D:199 , PHE D:203 , HOH D:1009BINDING SITE FOR RESIDUE HEM D 300
10BC1SOFTWARETYR D:156 , PHE D:203BINDING SITE FOR RESIDUE IPA D 1004
11BC2SOFTWARETYR C:156 , HOH C:1072BINDING SITE FOR RESIDUE IPA C 1003
12BC3SOFTWAREPHE B:203BINDING SITE FOR RESIDUE IPA B 1002
13BC4SOFTWAREPHE A:29 , LEU A:42BINDING SITE FOR RESIDUE IPA A 1001
14BC5SOFTWAREGLU A:54 , MET A:57 , ILE A:69 , TYR A:70 , PHE A:71 , ASN A:75 , TYR A:128BINDING SITE FOR RESIDUE IPA A 1005
15BC6SOFTWAREMET B:57 , ILE B:69 , TYR B:70 , PHE B:71 , LEU B:74 , SER B:124 , TYR B:128BINDING SITE FOR RESIDUE IPA B 1006
16BC7SOFTWAREMET C:57 , ILE C:69 , PHE C:71 , LEU C:74 , ASN C:75 , SER C:124BINDING SITE FOR RESIDUE IPA C 1007
17BC8SOFTWAREMET D:57 , ILE D:69 , TYR D:70 , PHE D:71 , ASN D:75 , SER D:124 , TYR D:128BINDING SITE FOR RESIDUE IPA D 1008

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WE1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WE1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WE1)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HO1_SYNY3120-130
 
 
 
  4A:120-130
B:120-130
C:120-130
D:120-130
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HO1_SYNY3120-130
 
 
 
  1A:120-130
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HO1_SYNY3120-130
 
 
 
  1-
B:120-130
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HO1_SYNY3120-130
 
 
 
  1-
-
C:120-130
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HO1_SYNY3120-130
 
 
 
  1-
-
-
D:120-130

(-) Exons   (0, 0)

(no "Exon" information available for 1WE1)

(-) Sequences/Alignments

Asymmetric 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:222
 aligned with HO1_SYNY3 | P72849 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
            HO1_SYNY3     2 SVNLASQLREGTKKSHSMAENVGFVKCFLKGVVEKNSYRKLVGNLYFVYSAMEEEMAKFKDHPILSHIYFPELNRKQSLEQDLQFYYGSNWRQEVKISAAGQAYVDRVRQVAATAPELLVAHSYTRYLGDLSGGQILKKIAQNAMNLHDGGTAFYEFADIDDEKAFKNTYRQAMNDLPIDQATAERIVDEANDAFAMNMKMFNELEGNLIKAIGIMVFNSLT 223
               SCOP domains d1we1a_ A: Heme oxygenase-1 (HO-1)                                                                                                                                                                                             SCOP domains
               CATH domains 1we1A00 A:2-223 Heme Oxygenase; Chain A                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN--------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1we1 A   2 SVNLASQLREGTKKSHSMAENVGFVKCFLKGVVEKNSYRKLVGNLYFVYSAMEEEMAKFKDHPILSHIYFPELNRKQSLEQDLQFYYGSNWRQEVKISAAGQAYVDRVRQVAATAPELLVAHSYTRYLGDLSGGQILKKIAQNAMNLHDGGTAFYEFADIDDEKAFKNTYRQAMNDLPIDQATAERIVDEANDAFAMNMKMFNELEGNLIKAIGIMVFNSLT 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with HO1_SYNY3 | P72849 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
            HO1_SYNY3     2 SVNLASQLREGTKKSHSMAENVGFVKCFLKGVVEKNSYRKLVGNLYFVYSAMEEEMAKFKDHPILSHIYFPELNRKQSLEQDLQFYYGSNWRQEVKISAAGQAYVDRVRQVAATAPELLVAHSYTRYLGDLSGGQILKKIAQNAMNLHDGGTAFYEFADIDDEKAFKNTYRQAMNDLPIDQATAERIVDEANDAFAMNMKMFNELEGNLIKAIGIMVFNSLT 223
               SCOP domains d1we1b_ B: Heme oxygenase-1 (HO-1)                                                                                                                                                                                             SCOP domains
               CATH domains 1we1B00 B:2-223 Heme Oxygenase; Chain A                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN--------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1we1 B   2 SVNLASQLREGTKKSHSMAENVGFVKCFLKGVVEKNSYRKLVGNLYFVYSAMEEEMAKFKDHPILSHIYFPELNRKQSLEQDLQFYYGSNWRQEVKISAAGQAYVDRVRQVAATAPELLVAHSYTRYLGDLSGGQILKKIAQNAMNLHDGGTAFYEFADIDDEKAFKNTYRQAMNDLPIDQATAERIVDEANDAFAMNMKMFNELEGNLIKAIGIMVFNSLT 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  

Chain C from PDB  Type:PROTEIN  Length:222
 aligned with HO1_SYNY3 | P72849 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
            HO1_SYNY3     2 SVNLASQLREGTKKSHSMAENVGFVKCFLKGVVEKNSYRKLVGNLYFVYSAMEEEMAKFKDHPILSHIYFPELNRKQSLEQDLQFYYGSNWRQEVKISAAGQAYVDRVRQVAATAPELLVAHSYTRYLGDLSGGQILKKIAQNAMNLHDGGTAFYEFADIDDEKAFKNTYRQAMNDLPIDQATAERIVDEANDAFAMNMKMFNELEGNLIKAIGIMVFNSLT 223
               SCOP domains d1we1c_ C: Heme oxygenase-1 (HO-1)                                                                                                                                                                                             SCOP domains
               CATH domains 1we1C00 C:2-223 Heme Oxygenase; Chain A                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN--------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1we1 C   2 SVNLASQLREGTKKSHSMAENVGFVKCFLKGVVEKNSYRKLVGNLYFVYSAMEEEMAKFKDHPILSHIYFPELNRKQSLEQDLQFYYGSNWRQEVKISAAGQAYVDRVRQVAATAPELLVAHSYTRYLGDLSGGQILKKIAQNAMNLHDGGTAFYEFADIDDEKAFKNTYRQAMNDLPIDQATAERIVDEANDAFAMNMKMFNELEGNLIKAIGIMVFNSLT 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  

Chain D from PDB  Type:PROTEIN  Length:221
 aligned with HO1_SYNY3 | P72849 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
            HO1_SYNY3     3 VNLASQLREGTKKSHSMAENVGFVKCFLKGVVEKNSYRKLVGNLYFVYSAMEEEMAKFKDHPILSHIYFPELNRKQSLEQDLQFYYGSNWRQEVKISAAGQAYVDRVRQVAATAPELLVAHSYTRYLGDLSGGQILKKIAQNAMNLHDGGTAFYEFADIDDEKAFKNTYRQAMNDLPIDQATAERIVDEANDAFAMNMKMFNELEGNLIKAIGIMVFNSLT 223
               SCOP domains d1we1d_ D: Heme oxygenase-1 (HO-1)                                                                                                                                                                                            SCOP domains
               CATH domains 1we1D00 D:3-223 Heme Oxygenase; Chain A                                                                                                                                                                                       CATH domains
           Pfam domains (1) Heme_oxygenase-1we1D01 D:3-205                                                                                                                                                                             ------------------ Pfam domains (1)
           Pfam domains (2) Heme_oxygenase-1we1D02 D:3-205                                                                                                                                                                             ------------------ Pfam domains (2)
           Pfam domains (3) Heme_oxygenase-1we1D03 D:3-205                                                                                                                                                                             ------------------ Pfam domains (3)
           Pfam domains (4) Heme_oxygenase-1we1D04 D:3-205                                                                                                                                                                             ------------------ Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------HEME_OXYGEN--------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1we1 D   3 VNLASQLREGTKKSHSMAENVGFVKCFLKGVVEKNSYRKLVGNLYFVYSAMEEEMAKFKDHPILSHIYFPELNRKQSLEQDLQFYYGSNWRQEVKISAAGQAYVDRVRQVAATAPELLVAHSYTRYLGDLSGGQILKKIAQNAMNLHDGGTAFYEFADIDDEKAFKNTYRQAMNDLPIDQATAERIVDEANDAFAMNMKMFNELEGNLIKAIGIMVFNSLT 223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HO (49)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (HO1_SYNY3 | P72849)
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.
    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.
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.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.

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