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PDBsum entry 1hrk

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Lyase PDB id
1hrk
Jmol
Contents
Protein chain
359 a.a. *
Ligands
CHD ×6
FES ×2
Waters ×596
* Residue conservation analysis
PDB id:
1hrk
Name: Lyase
Title: Crystal structure of human ferrochelatase
Structure: Ferrochelatase. Chain: a, b. Fragment: mature length. Synonym: protoheme ferro-lyase, heme synthetase. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.202     R-free:   0.226
Authors: C.K.Wu,H.A.Dailey,J.P.Rose,A.Burden,V.M.Sellers,B.-C.Wang
Key ref:
C.K.Wu et al. (2001). The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis. Nat Struct Biol, 8, 156-160. PubMed id: 11175906 DOI: 10.1038/84152
Date:
21-Dec-00     Release date:   22-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P22830  (HEMH_HUMAN) -  Ferrochelatase, mitochondrial
Seq:
Struc:
423 a.a.
359 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.99.1.1  - Ferrochelatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Heme and Chlorophyll Biosynthesis
      Reaction: Protoheme + 2 H+ = protoporphyrin + Fe2+
Protoheme
+ 2 × H(+)
=
protoporphyrin
Bound ligand (Het Group name = CHD)
matches with 57.00% similarity
+ Fe(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     heme biosynthetic process   1 term 
  Biochemical function     ferrochelatase activity     1 term  

 

 
    Added reference    
 
 
DOI no: 10.1038/84152 Nat Struct Biol 8:156-160 (2001)
PubMed id: 11175906  
 
 
The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis.
C.K.Wu, H.A.Dailey, J.P.Rose, A.Burden, V.M.Sellers, B.C.Wang.
 
  ABSTRACT  
 
Human ferrochelatase (E.C. 4.99.1.1) is a homodimeric (86 kDa) mitochondrial membrane-associated enzyme that catalyzes the insertion of ferrous iron into protoporphyrin to form heme. We have determined the 2.0 A structure from the single wavelength iron anomalous scattering signal. The enzyme contains two NO-sensitive and uniquely coordinated [2Fe-2S] clusters. Its membrane association is mediated in part by a 12-residue hydrophobic lip that also forms the entrance to the active site pocket. The positioning of highly conserved residues in the active site in conjunction with previous biochemical studies support a catalytic model that may have significance in explaining the enzymatic defects that lead to the human inherited disease erythropoietic protoporphyria.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structural features of HFc. a, Stereo view showing the structure of HFc (prepared using MOLSCRIPT28). The polypeptide is folded into two similar / domains. The structure includes 17 helices ( 1 - 17) and eight -sheets ( 1 - 8). The [2Fe-2S] cluster is coordinated by residues Cys 403, Cys 406, and Cys 411 in the C-terminal extension and Cys 196 in the N-terminal domain. The positions of the putative ferrous iron binding sites are shown as red balls. Three detergent molecule cholates (CHO1, CHO2, CHO3) were found in the binding pocket. b, Topology of HFc, with the N-terminus in yellow, C-terminus in blue and C-terminal extension in pink. c, Overlay of the N-terminal domain on the C-terminal domain. The r.m.s. deviation for 105 common C atoms is 3.1 . The major differences between the two domains include the N-terminal section (residues 80 -130) and a C-terminal extension consisting of residues 390 -423, which form the binding motif for the [2Fe-2S] cluster. The helices 8 and 15 are in a hinge region similar to that found in the periplasmic binding proteins. d, Sequence and secondary structure alignments29, 30 for human, Drosophila melanogaster, Saccharomyces cerevisiae (yeast), and B. subtilis ferrochelatases. Residues with a red background are conserved among all four sequences. Mammalian, fly, and yeast ferrochelatases have N-terminal mitochondrial targeting sequences and C-terminal extensions that are not present in BFc. The most significant structural variation between eukaryotic ferrochelatases and BFc is at the helix 2 region where the eukaryotic ferrochelatases have an additional 13 amino acids. e, Stereo view showing the refined (2F[o] - F[c]) electron density (contoured at 1 ) of active site residues near His 263.
Figure 3.
Figure 3. A sectional view of the HFc active site pocket shown as a, a cartoon drawing and b, a ribbon drawing. The lip regions (green) of the binding pocket are rich in hydrophobic residues (yellow) and the interior or the base of the pocket is populated with mostly hydrophilic residues (red). The three detergent molecules (gray) extend from the protein surface to the inside of the active site pocket in alternating (head to tail) conformations (the dot in CHO2 denotes facing inward) and define a curved pathway. The length of the dashed line beneath CHO1 is the approximate linear dimension of the porphyrin macrocycle. The conserved residues (circled by black dashed lines) located on the lower lip and the base of the pocket include His 263, Glu 343, His 341 and Phe 337 on one side, and Tyr 123, Arg 164 and Tyr165 on the other side. His 263 and Tyr 165 are opposite one another in the pocket. The hydrophobic residues in the lower lip are linearly arranged like teeth intercalating between the cholates. The highly conserved residues Tyr 165 and Arg 164 are circled by blue dashed lines. In the proposed catalytic model of HFc, the porphyrin entry pathway follows the cholate molecule positions to the pocket interior. The residues His 263, Glu 343, and Asp 340 are proposed to be involved in the two-proton extraction from the pyrrole nitrogens. The iron entry may occur from the cobalt binding site at His 230/Asp 383, which is located below the bottom of this diagram. The final metallation may occur from Arg 164 and Tyr 165, which are on the opposite side of the pocket from His 263. c, Electron density (contoured at 1 ) surrounding the cobalt binding site. The metal ion is coordinated by residues His 231 and Asp 383. The site is located on the surface of the protein opposite the active site containing surface.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 156-160) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21173279 C.V.Romão, D.Ladakis, S.A.Lobo, M.A.Carrondo, A.A.Brindley, E.Deery, P.M.Matias, R.W.Pickersgill, L.M.Saraiva, and M.J.Warren (2011).
Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization.
  Proc Natl Acad Sci U S A, 108, 97.
PDB codes: 2xvx 2xvz 2xwp 2xwq 2xws
21052751 M.D.Hansson, T.Karlberg, C.A.Söderberg, S.Rajan, M.J.Warren, S.Al-Karadaghi, S.E.Rigby, and M.Hansson (2011).
Bacterial ferrochelatase turns human: Tyr13 determines the apparent metal specificity of Bacillus subtilis ferrochelatase.
  J Biol Inorg Chem, 16, 235-242.  
21222436 N.R.McIntyre, R.Franco, J.A.Shelnutt, and G.C.Ferreira (2011).
Nickel(II) chelatase variants directly evolved from murine ferrochelatase: porphyrin distortion and kinetic mechanism.
  Biochemistry, 50, 1535-1544.  
19965627 D.R.Crooks, M.C.Ghosh, R.G.Haller, W.H.Tong, and T.A.Rouault (2010).
Posttranslational stability of the heme biosynthetic enzyme ferrochelatase is dependent on iron availability and intact iron-sulfur cluster assembly machinery.
  Blood, 115, 860-869.  
20506125 G.Layer, J.Reichelt, D.Jahn, and D.W.Heinz (2010).
Structure and function of enzymes in heme biosynthesis.
  Protein Sci, 19, 1137-1161.  
20823222 K.Kato, R.Tanaka, S.Sano, A.Tanaka, and H.Hosaka (2010).
Identification of a gene essential for protoporphyrinogen IX oxidase activity in the cyanobacterium Synechocystis sp. PCC6803.
  Proc Natl Acad Sci U S A, 107, 16649-16654.  
  20463401 M.P.Horowitz, and J.T.Greenamyre (2010).
Mitochondrial iron metabolism and its role in neurodegeneration.
  J Alzheimers Dis, 20, S551-S568.  
20427704 W.Chen, H.A.Dailey, and B.H.Paw (2010).
Ferrochelatase forms an oligomeric complex with mitoferrin-1 and Abcb10 for erythroid heme biosynthesis.
  Blood, 116, 628-630.  
19543923 B.Szefczyk, M.N.Cordeiro, R.Franco, and J.A.Gomes (2009).
Molecular dynamics simulations of mouse ferrochelatase variants: what distorts and orientates the porphyrin?
  J Biol Inorg Chem, 14, 1119-1128.  
19021503 F.W.Outten, and E.C.Theil (2009).
Iron-based redox switches in biology.
  Antioxid Redox Signal, 11, 1029-1046.  
19767646 R.E.Davidson, C.J.Chesters, and J.D.Reid (2009).
Metal ion selectivity and substrate inhibition in the metal ion chelation catalyzed by human ferrochelatase.
  J Biol Chem, 284, 33795-33799.  
18787536 S.A.Holme, S.D.Whatley, A.G.Roberts, A.V.Anstey, G.H.Elder, R.D.Ead, M.F.Stewart, P.M.Farr, H.M.Lewis, N.Davies, M.I.White, R.S.Ackroyd, and M.N.Badminton (2009).
Seasonal palmar keratoderma in erythropoietic protoporphyria indicates autosomal recessive inheritance.
  J Invest Dermatol, 129, 599-605.  
19656484 T.A.Rouault, and W.H.Tong (2009).
Tangled up in red: intertwining of the heme and iron-sulfur cluster biogenesis pathways.
  Cell Metab, 10, 80-81.  
19381358 V.Hower, P.Mendes, F.M.Torti, R.Laubenbacher, S.Akman, V.Shulaev, and S.V.Torti (2009).
A general map of iron metabolism and tissue-specific subnetworks.
  Mol Biosyst, 5, 422-443.  
19047738 A.Masoumi, I.U.Heinemann, M.Rohde, M.Koch, M.Jahn, and D.Jahn (2008).
Complex formation between protoporphyrinogen IX oxidase and ferrochelatase during haem biosynthesis in Thermosynechococcus elongatus.
  Microbiology, 154, 3707-3714.  
18593702 G.A.Hunter, M.P.Sampson, and G.C.Ferreira (2008).
Metal ion substrate inhibition of ferrochelatase.
  J Biol Chem, 283, 23685-23691.  
  19787086 J.Bloomer, Y.Wang, and D.Chen (2008).
Level of Expression of the Nonmutant Ferrochelatase Allele is a Determinant of Biochemical Phenotype in a Mouse Model of Erythropoietic Protoporphyria.
  Gene Regul Syst Bio, 2, 233-241.  
18192382 R.Sobotka, S.McLean, M.Zuberova, C.N.Hunter, and M.Tichy (2008).
The C-terminal extension of ferrochelatase is critical for enzyme activity and for functioning of the tetrapyrrole pathway in Synechocystis strain PCC 6803.
  J Bacteriol, 190, 2086-2095.  
18423489 T.Karlberg, M.D.Hansson, R.K.Yengo, R.Johansson, H.O.Thorvaldsen, G.C.Ferreira, M.Hansson, and S.Al-Karadaghi (2008).
Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues.
  J Mol Biol, 378, 1074-1083.
PDB codes: 2q2n 2q2o 2q3j
18846277 T.Masuda, and Y.Fujita (2008).
Regulation and evolution of chlorophyll metabolism.
  Photochem Photobiol Sci, 7, 1131-1149.  
17884090 A.E.Medlock, T.A.Dailey, T.A.Ross, H.A.Dailey, and W.N.Lanzilotta (2007).
A pi-helix switch selective for porphyrin deprotonation and product release in human ferrochelatase.
  J Mol Biol, 373, 1006-1016.
PDB codes: 2qd1 2qd2 2qd3 2qd4 2qd5
17603894 A.L.Lomize, I.D.Pogozheva, M.A.Lomize, and H.I.Mosberg (2007).
The role of hydrophobic interactions in positioning of peripheral proteins in membranes.
  BMC Struct Biol, 7, 44.  
17261801 A.Medlock, L.Swartz, T.A.Dailey, H.A.Dailey, and W.N.Lanzilotta (2007).
Substrate interactions with human ferrochelatase.
  Proc Natl Acad Sci U S A, 104, 1789-1793.
PDB codes: 2hrc 2hre
17665226 B.N.Hudder, J.G.Morales, A.Stubna, E.Münck, M.P.Hendrich, and P.A.Lindahl (2007).
Electron paramagnetic resonance and Mössbauer spectroscopy of intact mitochondria from respiring Saccharomyces cerevisiae.
  J Biol Inorg Chem, 12, 1029-1053.  
17567154 H.A.Dailey, C.K.Wu, P.Horanyi, A.E.Medlock, W.Najahi-Missaoui, A.E.Burden, T.A.Dailey, and J.Rose (2007).
Altered orientation of active site residues in variants of human ferrochelatase. Evidence for a hydrogen bond network involved in catalysis.
  Biochemistry, 46, 7973-7979.
PDB codes: 2pnj 2po5 2po7
17476391 K.Z.Bencze, T.Yoon, C.Millán-Pacheco, P.B.Bradley, N.Pastor, J.A.Cowan, and T.L.Stemmler (2007).
Human frataxin: iron and ferrochelatase binding surface.
  Chem Commun (Camb), (), 1798-1800.  
17227226 R.Tanaka, and A.Tanaka (2007).
Tetrapyrrole biosynthesis in higher plants.
  Annu Rev Plant Biol, 58, 321-346.  
16835730 J.Yin, L.X.Xu, M.M.Cherney, E.Raux-Deery, A.A.Bindley, A.Savchenko, J.R.Walker, M.E.Cuff, M.J.Warren, and M.N.James (2006).
Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus.
  J Struct Funct Genomics, 7, 37-50.
PDB code: 2dj5
16911956 K.Z.Bencze, K.C.Kondapalli, J.D.Cook, S.McMahon, C.Millán-Pacheco, N.Pastor, and T.L.Stemmler (2006).
The structure and function of frataxin.
  Crit Rev Biochem Mol Biol, 41, 269-291.  
16453119 M.D.Hansson, M.Lindstam, and M.Hansson (2006).
Crosstalk between metal ions in Bacillus subtilis ferrochelatase.
  J Biol Inorg Chem, 11, 325-333.  
16453120 P.M.Rodrigues, A.L.Macedo, B.J.Goodfellow, I.Moura, and J.J.Moura (2006).
Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe-4S] cluster.
  J Biol Inorg Chem, 11, 307-315.  
16469498 S.Al-Karadaghi, R.Franco, M.Hansson, J.A.Shelnutt, G.Isaya, and G.C.Ferreira (2006).
Chelatases: distort to select?
  Trends Biochem Sci, 31, 135-142.  
16339726 A.Atteia, R.van Lis, and S.I.Beale (2005).
Enzymes of the heme biosynthetic pathway in the nonphotosynthetic alga Polytomella sp.
  Eukaryot Cell, 4, 2087-2097.  
15952888 D.C.Johnson, D.R.Dean, A.D.Smith, and M.K.Johnson (2005).
Structure, function, and formation of biological iron-sulfur clusters.
  Annu Rev Biochem, 74, 247-281.  
15831703 S.S.Cooperman, E.G.Meyron-Holtz, H.Olivierre-Wilson, M.C.Ghosh, J.P.McConnell, and T.A.Rouault (2005).
Microcytic anemia, erythropoietic protoporphyria, and neurodegeneration in mice with targeted deletion of iron-regulatory protein 2.
  Blood, 106, 1084-1091.  
15831704 W.Najahi-Missaoui, and H.A.Dailey (2005).
Production and characterization of erythropoietic protoporphyric heterodimeric ferrochelatases.
  Blood, 106, 1098-1104.  
15662683 Y.Shen, and U.Ryde (2005).
Reaction mechanism of porphyrin metallation studied by theoretical methods.
  Chemistry, 11, 1549-1564.  
15057273 M.Koch, C.Breithaupt, R.Kiefersauer, J.Freigang, R.Huber, and A.Messerschmidt (2004).
Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis.
  EMBO J, 23, 1720-1728.
PDB code: 1sez
15123683 T.Yoon, and J.A.Cowan (2004).
Frataxin-mediated iron delivery to ferrochelatase in the final step of heme biosynthesis.
  J Biol Chem, 279, 25943-25946.  
15610019 Y.He, S.L.Alam, S.V.Proteasa, Y.Zhang, E.Lesuisse, A.Dancis, and T.L.Stemmler (2004).
Yeast frataxin solution structure, iron binding, and ferrochelatase interaction.
  Biochemistry, 43, 16254-16262.
PDB codes: 1xaq 2ga5
14981080 Z.Shi, and G.C.Ferreira (2004).
Probing the active site loop motif of murine ferrochelatase by random mutagenesis.
  J Biol Chem, 279, 19977-19986.  
12758040 J.E.Cornah, M.J.Terry, and A.G.Smith (2003).
Green or red: what stops the traffic in the tetrapyrrole pathway?
  Trends Plant Sci, 8, 224-230.  
12732649 S.Park, O.Gakh, H.A.O'Neill, A.Mangravita, H.Nichol, G.C.Ferreira, and G.Isaya (2003).
Yeast frataxin sequentially chaperones and stores iron by coupling protein assembly with iron oxidation.
  J Biol Chem, 278, 31340-31351.  
12010463 D.V.Vavilin, and W.F.Vermaas (2002).
Regulation of the tetrapyrrole biosynthetic pathway leading to heme and chlorophyll in plants and cyanobacteria.
  Physiol Plant, 115, 9.  
11939775 G.C.Ferreira, R.Franco, A.Mangravita, and G.N.George (2002).
Unraveling the substrate-metal binding site of ferrochelatase: an X-ray absorption spectroscopic study.
  Biochemistry, 41, 4809-4818.  
11980703 H.L.Schubert, E.Raux, A.A.Brindley, H.K.Leech, K.S.Wilson, C.P.Hill, and M.J.Warren (2002).
The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase.
  EMBO J, 21, 2068-2075.
PDB code: 1kyq
11863449 J.Meyer, M.D.Clay, M.K.Johnson, A.Stubna, E.Münck, C.Higgins, and P.Wittung-Stafshede (2002).
A hyperthermophilic plant-type [2Fe-2S] ferredoxin from Aquifex aeolicus is stabilized by a disulfide bond.
  Biochemistry, 41, 3096-3108.  
11948160 T.A.Dailey, and H.A.Dailey (2002).
Identification of [2Fe-2S] clusters in microbial ferrochelatases.
  J Bacteriol, 184, 2460-2464.  
12081974 U.Olsson, A.Billberg, S.Sjövall, S.Al-Karadaghi, and M.Hansson (2002).
In vivo and in vitro studies of Bacillus subtilis ferrochelatase mutants suggest substrate channeling in the heme biosynthesis pathway.
  J Bacteriol, 184, 4018-4024.  
12081474 Y.Lu, A.Sousa, R.Franco, A.Mangravita, G.C.Ferreira, I.Moura, and J.A.Shelnutt (2002).
Binding of protoporphyrin IX and metal derivatives to the active site of wild-type mouse ferrochelatase at low porphyrin-to-protein ratios.
  Biochemistry, 41, 8253-8262.  
11506917 K.F.Wang, T.A.Dailey, and H.A.Dailey (2001).
Expression and characterization of the terminal heme synthetic enzymes from the hyperthermophile Aquifex aeolicus.
  FEMS Microbiol Lett, 202, 115-119.  
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 codes are shown on the right.