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(-) Description

Title :  ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF HUMAN HEME OXYGENASE-2 C127A (HO-2) WITH BOUND HEME
 
Authors :  C. M. Bianchetti, C. A. Bingman, E. Bitto, G. E. Wesenberg, G. N. Phillip Center For Eukaryotic Structural Genomics (Cesg)
Date :  05 Oct 07  (Deposition) - 23 Oct 07  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A,B  (16x)
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, Structural Genomics Medical Relevance, Structural Genomics Community Request, Ho-2, Heme Oxygenase, Endoplasmic Reticulum, Iron, Metal-Binding, Microsome, Oxidoreductase, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. M. Bianchetti, L. Yi, S. W. Ragsdale, G. N. Phillips Jr.
Comparison Of Apo- And Heme-Bound Crystal Structures Of A Truncated Human Heme Oxygenase-2.
J. Biol. Chem. V. 282 37624 2007
PubMed-ID: 17965015  |  Reference-DOI: 10.1074/JBC.M707396200

(-) Compounds

Molecule 1 - HEME OXYGENASE 2
    ChainsA, B
    EC Number1.14.99.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX 4T-2
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneHMOX2, HO2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHO-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit (16x)AB
Biological Unit 1 (1x)AB
Biological Unit 2 (1x)A 
Biological Unit 3 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:45 , ALA A:48 , GLU A:49 , VAL A:54 , LEU A:58 , TYR A:154 , THR A:155 , ARG A:156 , GLY A:159 , SER A:162 , LYS A:199 , ARG A:203 , PHE A:227 , ASN A:230 , PHE A:234 , HOH A:319BINDING SITE FOR RESIDUE HEM A 300
2AC2SOFTWAREHIS B:45 , VAL B:54 , LEU B:58 , TYR B:154 , THR B:155 , ARG B:156 , MET B:158 , GLY B:159 , SER B:162 , ARG B:203 , PHE B:227 , PHE B:234BINDING SITE FOR RESIDUE HEM B 265

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RGZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RGZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021067R137QHMOX2_HUMANPolymorphism17884623A/BR137Q
2UniProtVAR_021068P146LHMOX2_HUMANPolymorphism17880805A/BP146L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021067R137QHMOX2_HUMANPolymorphism17884623A/BR137Q
2UniProtVAR_021068P146LHMOX2_HUMANPolymorphism17880805A/BP146L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021067R137QHMOX2_HUMANPolymorphism17884623AR137Q
2UniProtVAR_021068P146LHMOX2_HUMANPolymorphism17880805AP146L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021067R137QHMOX2_HUMANPolymorphism17884623BR137Q
2UniProtVAR_021068P146LHMOX2_HUMANPolymorphism17880805BP146L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HMOX2_HUMAN149-159
 
  2A:149-159
B:149-159
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HMOX2_HUMAN149-159
 
  2A:149-159
B:149-159
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HMOX2_HUMAN149-159
 
  1A:149-159
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HMOX2_HUMAN149-159
 
  1-
B:149-159

(-) Exons   (4, 7)

Asymmetric Unit (4, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000002197002bENSE00001301100chr16:4526380-4526488109HMOX2_HUMAN-00--
1.5aENST000002197005aENSE00001010603chr16:4555485-4555611127HMOX2_HUMAN1-29291A:29-29
-
1
-
1.6ENST000002197006ENSE00000667221chr16:4556896-4557013118HMOX2_HUMAN29-68402A:29-68
B:30-68
40
39
1.7ENST000002197007ENSE00000667220chr16:4557714-4558205492HMOX2_HUMAN69-2321642A:69-232
B:69-232
164
164
1.8ENST000002197008ENSE00000667219chr16:4559413-4559539127HMOX2_HUMAN233-275432A:233-242
B:233-248
10
16
1.9cENST000002197009cENSE00001818091chr16:4559630-4560348719HMOX2_HUMAN275-316420--

(-) 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:214
 aligned with HMOX2_HUMAN | P30519 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:214
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238    
          HMOX2_HUMAN    29 RMADLSELLKEGTKEAHDRAENTQFVKDFLKGNIKKELFKLATTALYFTYSALEEEMERNKDHPAFAPLYFPMELHRKEALTKDMEYFFGENWEEQVQCPKAAQKYVERIHYIGQNEPELLVAHAYTRYMGDLSGGQVLKKVAQRALKLPSTGEGTQFYLFENVDNAQQFKQLYRARMNALDLNMKTKERIVEEANKAFEYNMQIFNELDQAGS 242
               SCOP domains d2rgza_ A: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 2rgzA00 A:29-242 Heme Oxygenase; Chain A                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------Q--------L------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------HEME_OXYGEN----------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1---------------------------------------Exon 1.7  PDB: A:69-232 UniProt: 69-232                                                                                                                             Exon 1.8   Transcript 1 (1)
           Transcript 1 (2) Exon 1.6  PDB: A:29-68 UniProt: 29-68   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2rgz A  29 RMADLSELLKEGTKEAHDRAENTQFVKDFLKGNIKKELFKLATTALYFTYSALEEEMERNKDHPAFAPLYFPMELHRKEALTKDMEYFFGENWEEQVQAPKAAQKYVERIHYIGQNEPELLVAHAYTRYMGDLSGGQVLKKVAQRALKLPSTGEGTQFYLFENVDNAQQFKQLYRARMNALDLNMKTKERIVEEANKAFEYNMQIFNELDQAGS 242
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238    

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with HMOX2_HUMAN | P30519 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:219
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239         
          HMOX2_HUMAN    30 MADLSELLKEGTKEAHDRAENTQFVKDFLKGNIKKELFKLATTALYFTYSALEEEMERNKDHPAFAPLYFPMELHRKEALTKDMEYFFGENWEEQVQCPKAAQKYVERIHYIGQNEPELLVAHAYTRYMGDLSGGQVLKKVAQRALKLPSTGEGTQFYLFENVDNAQQFKQLYRARMNALDLNMKTKERIVEEANKAFEYNMQIFNELDQAGSTLARET 248
               SCOP domains d2rgzb_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains 2rgzB00 B:30-248 Heme Oxygenase; Chain A                                                                                                                                                                                    CATH domains
           Pfam domains (1) -Heme_oxygenase-2rgzB01 B:31-236                                                                                                                                                                               ------------ Pfam domains (1)
           Pfam domains (2) -Heme_oxygenase-2rgzB02 B:31-236                                                                                                                                                                               ------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhh........hhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------Q--------L------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN----------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ---------------------------------------Exon 1.7  PDB: B:69-232 UniProt: 69-232                                                                                                                             Exon 1.8         Transcript 1 (1)
           Transcript 1 (2) Exon 1.6  PDB: B:30-68 UniProt: 29-68  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2rgz B  30 MADLSELLKEGTKEAHDRAENTQFVKDFLKGNIKKELFKLATTALYFTYSALEEEMERNKDHPAFAPLYFPMELHRKEALTKDMEYFFGENWEEQVQAPKAAQKYVERIHYIGQNEPELLVAHAYTRYMGDLSGGQVLKKVAQRALKLPSTGEGTQFYLFENVDNAQQFKQLYRARMNALDLNMKTKERIVEEANKAFEYNMQIFNELDQAGSTLARET 248
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239         

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HO (49)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HMOX2_HUMAN | P30519)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    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: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:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HMOX2_HUMAN | P305192q32 2qpp 4wmh 5uc8 5uc9 5uca

(-) Related Entries Specified in the PDB File

2q32 HUMAN HEME OXYGENASE-2 C127A (HO-2) WITHOUT BOUND HEME.
2qpp ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.