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PDBsum entry 1irm

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protein Protein-protein interface(s) links
Oxidoreductase PDB id
1irm
Jmol
Contents
Protein chains
196 a.a. *
Waters ×87
* Residue conservation analysis
PDB id:
1irm
Name: Oxidoreductase
Title: Crystal structure of apo heme oxygenase-1
Structure: Apo heme oxygenase-1. Chain: c, a, b. Fragment: residues 1-267. Synonym: ho-1. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.55Å     R-factor:   0.202     R-free:   0.307
Authors: M.Sugishima,H.Sakamoto,Y.Kakuta,Y.Omata,S.Hayashi,M.Noguchi, K.Fukuyama
Key ref:
M.Sugishima et al. (2002). Crystal structure of rat apo-heme oxygenase-1 (HO-1): mechanism of heme binding in HO-1 inferred from structural comparison of the apo and heme complex forms. Biochemistry, 41, 7293-7300. PubMed id: 12044160 DOI: 10.1021/bi025662a
Date:
09-Oct-01     Release date:   10-Jul-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06762  (HMOX1_RAT) -  Heme oxygenase 1
Seq:
Struc:
289 a.a.
196 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.99.3  - Heme oxygenase (biliverdin-producing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protoheme + 3 AH2 + 3 O2 = biliverdin + Fe2+ + CO + 3 A + 3 H2O
Protoheme
+ 3 × AH(2)
+ 3 × O(2)
= biliverdin
+ Fe(2+)
+ CO
+ 3 × A
+ 3 × H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   9 terms 
  Biological process     intracellular signal transduction   40 terms 
  Biochemical function     signal transducer activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi025662a Biochemistry 41:7293-7300 (2002)
PubMed id: 12044160  
 
 
Crystal structure of rat apo-heme oxygenase-1 (HO-1): mechanism of heme binding in HO-1 inferred from structural comparison of the apo and heme complex forms.
M.Sugishima, H.Sakamoto, Y.Kakuta, Y.Omata, S.Hayashi, M.Noguchi, K.Fukuyama.
 
  ABSTRACT  
 
Heme oxygenase (HO) catalyzes the oxidative cleavage of heme to biliverdin by utilizing O(2) and NADPH. HO (apoHO) was crystallized as twinned P3(2) with three molecules per asymmetric unit, and its crystal structure was determined at 2.55 A resolution. Structural comparison of apoHO and its complex with heme (HO-heme) showed three distinct differences. First, the A helix of the eight alpha-helices (A-H) in HO-heme, which includes the proximal ligand of heme (His25), is invisible in apoHO. In addition, the B helix, a portion of which builds the heme pocket, is shifted toward the heme pocket in apoHO. Second, Gln38 is shifted toward the position where the alpha-meso carbon of heme is located in HO-heme. Nepsilon of Gln38 is hydrogen-bonded to the carbonyl group of Glu29 located at the C-terminal side of the A helix in HO-heme, indicative that this hydrogen bond restrains the angle between the A and B helices in HO-heme. Third, the amide group of Gly143 in the F helix is directed outward from the heme pocket in apoHO, whereas it is directed toward the distal ligand of heme in HO-heme. This means that the F helix around Gly143 must change its conformation to accommodate heme binding. The apoHO structure has the characteristic that the helix on one side of the heme pocket fluctuates, whereas the rest of the structure is similar to that of HO-heme, as observed in such hemoproteins as myoglobin and cytochromes b(5) and b(562). These structural features of apoHO suggest that the orientation of the proximal helix and the position of His25 are fixed upon heme binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21283550 C.Tuzmen, and B.Erman (2011).
Identification of ligand binding sites of proteins using the gaussian network model.
  PLoS One, 6, e16474.  
19243105 H.Ogura, J.P.Evans, D.Peng, J.D.Satterlee, P.R.Ortiz de Montellano, and G.N.La Mar (2009).
The orbital ground state of the azide-substrate complex of human heme oxygenase is an indicator of distal H-bonding: implications for the enzyme mechanism.
  Biochemistry, 48, 3127-3137.  
19123922 W.J.Huber Iii, B.A.Scruggs, and W.L.Backes (2009).
C-Terminal membrane spanning region of human heme oxygenase-1 mediates a time-dependent complex formation with cytochrome P450 reductase.
  Biochemistry, 48, 190-197.  
18286277 J.D.Maréchal, and D.Perahia (2008).
Use of normal modes for structural modeling of proteins: the case study of rat heme oxygenase 1.
  Eur Biophys J, 37, 1157-1165.  
18092096 N.Yokoi, T.Ueno, M.Unno, T.Matsui, M.Ikeda-Saito, and Y.Watanabe (2008).
Ligand design for the improvement of stability of metal complex.protein hybrids.
  Chem Commun (Camb), (), 229-231.
PDB code: 2z68
  18607087 P.Fernández-Millán, D.Kortazar, M.Lucas, M.L.Martínez-Chantar, E.Astigarraga, J.A.Fernández, O.Sabas, A.Albert, J.M.Mato, and L.A.Martínez-Cruz (2008).
Crystallization and preliminary crystallographic analysis of merohedrally twinned crystals of MJ0729, a CBS-domain protein from Methanococcus jannaschii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 605-609.  
18194664 Y.Higashimoto, M.Sugishima, H.Sato, H.Sakamoto, K.Fukuyama, G.Palmer, and M.Noguchi (2008).
Mass spectrometric identification of lysine residues of heme oxygenase-1 that are involved in its interaction with NADPH-cytochrome P450 reductase.
  Biochem Biophys Res Commun, 367, 852-858.  
17965015 C.M.Bianchetti, L.Yi, S.W.Ragsdale, and G.N.Phillips (2007).
Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2.
  J Biol Chem, 282, 37624-37631.
PDB codes: 2q32 2qpp 2rgz
17550789 D.A.Landfried, D.A.Vuletich, M.P.Pond, and J.T.Lecomte (2007).
Structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins.
  Gene, 398, 12-28.  
17534530 M.Unno, T.Matsui, and M.Ikeda-Saito (2007).
Structure and catalytic mechanism of heme oxygenase.
  Nat Prod Rep, 24, 553-570.  
17443801 T.Watanabe, M.Kikuchi, D.Hatakeyama, T.Shiga, T.Yamamoto, H.Aonuma, M.Takahata, N.Suzuki, and E.Ito (2007).
Gaseous neuromodulator-related genes expressed in the brain of honeybee Apis mellifera.
  Dev Neurobiol, 67, 456-473.  
16928691 Y.Higashimoto, H.Sato, H.Sakamoto, K.Takahashi, G.Palmer, and M.Noguchi (2006).
The reactions of heme- and verdoheme-heme oxygenase-1 complexes with FMN-depleted NADPH-cytochrome P450 reductase. Electrons required for verdoheme oxidation can be transferred through a pathway not involving FMN.
  J Biol Chem, 281, 31659-31667.  
15690204 L.Lad, A.Koshkin, P.R.de Montellano, and T.L.Poulos (2005).
Crystal structures of the G139A, G139A-NO and G143H mutants of human heme oxygenase-1. A finely tuned hydrogen-bonding network controls oxygenase versus peroxidase activity.
  J Biol Inorg Chem, 10, 138-146.
PDB codes: 1xjz 1xk0 1xk1
15516695 Y.Higashimoto, H.Sakamoto, S.Hayashi, M.Sugishima, K.Fukuyama, G.Palmer, and M.Noguchi (2005).
Involvement of NADPH in the interaction between heme oxygenase-1 and cytochrome P450 reductase.
  J Biol Chem, 280, 729-737.  
15159569 H.Itou, M.Yao, N.Watanabe, and I.Tanaka (2004).
Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 60, 1094-1100.
PDB code: 1udd
14966119 M.Unno, T.Matsui, G.C.Chu, M.Couture, T.Yoshida, D.L.Rousseau, J.S.Olson, and M.Ikeda-Saito (2004).
Crystal structure of the dioxygen-bound heme oxygenase from Corynebacterium diphtheriae: implications for heme oxygenase function.
  J Biol Chem, 279, 21055-21061.
PDB code: 1v8x
14645223 S.Hirotsu, G.C.Chu, M.Unno, D.S.Lee, T.Yoshida, S.Y.Park, Y.Shiro, and M.Ikeda-Saito (2004).
The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae.
  J Biol Chem, 279, 11937-11947.
PDB codes: 1iw0 1iw1
14660632 Y.Li, R.T.Syvitski, K.Auclair, P.R.de Montellano, and G.N.La Mar (2004).
1H NMR investigation of the solution structure of substrate-free human heme oxygenase: comparison to the cyanide-inhibited, substrate-bound complex.
  J Biol Chem, 279, 10195-10205.  
12794075 M.Sugishima, H.Sakamoto, Y.Higashimoto, M.Noguchi, and K.Fukuyama (2003).
Crystal structure of rat heme oxygenase-1 in complex with biliverdin-iron chelate. Conformational change of the distal helix during the heme cleavage reaction.
  J Biol Chem, 278, 32352-32358.
PDB code: 1j2c
14514669 Y.H.Weng, G.Yang, S.Weiss, and P.A.Dennery (2003).
Interaction between heme oxygenase-1 and -2 proteins.
  J Biol Chem, 278, 50999-51005.  
12837796 Y.Shimomura, Y.Kakuta, and K.Fukuyama (2003).
Crystal structures of the quinone oxidoreductase from Thermus thermophilus HB8 and its complex with NADPH: implication for NADPH and substrate recognition.
  J Bacteriol, 185, 4211-4218.
PDB codes: 1iyz 1iz0
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.