spacer
spacer

PDBsum entry 1g8p

Go to PDB code: 
protein links
Photosynthesis, metal transport PDB id
1g8p
Jmol
Contents
Protein chain
321 a.a. *
Waters ×218
* Residue conservation analysis
PDB id:
1g8p
Name: Photosynthesis, metal transport
Title: Crystal structure of bchi subunit of magnesium chelatase
Structure: Magnesium-chelatase 38 kda subunit. Chain: a. Fragment: bchi subunit. Synonym: mg-protoporphyrin ix chelatase. Engineered: yes
Source: Rhodobacter capsulatus. Organism_taxid: 1061. Gene: bchi_rhoca. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.10Å     R-factor:   0.214     R-free:   0.247
Authors: M.N.Fodje,A.Hansson,M.Hansson,J.G.Olsen,S.Gough,R.D.Willows, S.Al-Karadaghi
Key ref:
M.N.Fodje et al. (2001). Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase. J Mol Biol, 311, 111-122. PubMed id: 11469861 DOI: 10.1006/jmbi.2001.4834
Date:
20-Nov-00     Release date:   03-Aug-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26239  (BCHI_RHOCB) -  Magnesium-chelatase 38 kDa subunit
Seq:
Struc:
350 a.a.
321 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.6.1.1  - Magnesium chelatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Heme and Chlorophyll Biosynthesis
      Reaction: ATP + protoporphyrin IX + Mg2+ + H2O = ADP + phosphate + Mg-protoporphyrin IX + 2 H+
ATP
+ protoporphyrin IX
+ Mg(2+)
+ H(2)O
= ADP
+ phosphate
+ Mg-protoporphyrin IX
+ 2 × H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     photosynthesis   4 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.4834 J Mol Biol 311:111-122 (2001)
PubMed id: 11469861  
 
 
Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase.
M.N.Fodje, A.Hansson, M.Hansson, J.G.Olsen, S.Gough, R.D.Willows, S.Al-Karadaghi.
 
  ABSTRACT  
 
In chlorophyll biosynthesis, insertion of Mg(2+) into protoporphyrin IX is catalysed in an ATP-dependent reaction by a three-subunit (BchI, BchD and BchH) enzyme magnesium chelatase. In this work we present the three-dimensional structure of the ATP-binding subunit BchI. The structure has been solved by the multiple wavelength anomalous dispersion method and refined at 2.1 A resolution to the crystallographic R-factor of 22.2 % (R(free)=24.5 %). It belongs to the chaperone-like "ATPase associated with a variety of cellular activities" (AAA) family of ATPases, with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide-binding site, while in other known AAA module structures it is located on the top. Examination by electron microscopy of BchI solutions in the presence of ATP demonstrated that BchI, like other AAA proteins, forms oligomeric ring structures. Analysis of the amino acid sequence of subunit BchD revealed an AAA module at the N-terminal portion of the sequence and an integrin I domain at the C terminus. An acidic, proline-rich region linking these two domains is suggested to contribute to the association of BchI and BchD by binding to a positively charged cleft at the surface of the nucleotide-binding domain of BchI. Analysis of the amino acid sequences of BchI and BchH revealed integrin I domain-binding sequence motifs. These are proposed to bind the integrin I domain of BchD during the functional cycle of magnesium chelatase, linking porphyrin metallation by BchH to ATP hydrolysis by BchI. An integrin I domain and an acidic and proline-rich region have been identified in subunit CobT of cobalt chelatase, clearly demonstrating its homology to BchD. These findings, for the first time, provide an insight into the subunit organisation of magnesium chelatase and the homologous colbalt chelatase.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Ribbon representation of the three-dimensional structure of BchI. The N-terminal domain is shown in grey, and the C-terminal domain in red. The P-loop, Walker B motif and the sensor 1 region are highlighted in gold, blue and purple, respectively. The part rendered in green shows insertions into the core AAA topology, specific to BchI. Helices and strands of the AAA core are numbered consecutively starting at the N terminus. Insertions are numbered i(1-3). The Figure was created with the program MOLSCRIPT.[51]
Figure 5.
Figure 5. (a) Superposition of the active sites of BchI (yellow) and HslU (grey). The ATP molecule from the HslU structure and BchI side-chain groups likely to be involved in ATP binding and/or hydrolysis are shown in ball-and-stick form. (b) Structure-based alignment of the Walker A, Walker B and sensor-1 motifs of BchI, NSF-D2, HslU and PIII-d'. Highly conserved positions are highlighted in black boxes and conserved substitutions in grey.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 311, 111-122) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21330489 A.P.Carter, C.Cho, L.Jin, and R.D.Vale (2011).
Crystal structure of the dynein motor domain.
  Science, 331, 1159-1165.
PDB code: 3qmz
20223218 J.Lundqvist, H.Elmlund, R.P.Wulff, L.Berglund, D.Elmlund, C.Emanuelsson, H.Hebert, R.D.Willows, M.Hansson, M.Lindahl, and S.Al-Karadaghi (2010).
ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase.
  Structure, 18, 354-365.
PDB code: 2x31
21148420 M.El Bakkouri, I.Gutsche, U.Kanjee, B.Zhao, M.Yu, G.Goret, G.Schoehn, W.P.Burmeister, and W.A.Houry (2010).
Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity.
  Proc Natl Acad Sci U S A, 107, 22499-22504.
PDB code: 3nbx
  20532744 S.Zappa, K.Li, and C.E.Bauer (2010).
The Tetrapyrrole Biosynthetic Pathway and Its Regulation in Rhodobacter capsulatus.
  Adv Exp Med Biol, 675, 229-250.  
19189964 A.Pelzmann, M.Ferner, M.Gnida, W.Meyer-Klaucke, T.Maisel, and O.Meyer (2009).
The CoxD protein of Oligotropha carboxidovorans is a predicted AAA+ ATPase chaperone involved in the biogenesis of the CO dehydrogenase [CuSMoO2] cluster.
  J Biol Chem, 284, 9578-9586.  
19217392 B.Bae, Y.H.Chen, A.Costa, S.Onesti, J.S.Brunzelle, Y.Lin, I.K.Cann, and S.K.Nair (2009).
Insights into the architecture of the replicative helicase from the structure of an archaeal MCM homolog.
  Structure, 17, 211-222.
PDB code: 3f8t
  19969518 J.Joyard, M.Ferro, C.Masselon, D.Seigneurin-Berny, D.Salvi, J.Garin, and N.Rolland (2009).
Chloroplast proteomics and the compartmentation of plastidial isoprenoid biosynthetic pathways.
  Mol Plant, 2, 1154-1180.  
19073923 A.S.Brewster, G.Wang, X.Yu, W.B.Greenleaf, J.M.Carazo, M.Tjajadia, M.G.Klein, and X.S.Chen (2008).
Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase.
  Proc Natl Acad Sci U S A, 105, 20191-20196.
PDB code: 3f9v
18790730 A.Sawicki, and R.D.Willows (2008).
Kinetic analyses of the magnesium chelatase provide insights into the mechanism, structure, and formation of the complex.
  J Biol Chem, 283, 31294-31302.  
18329872 E.J.Enemark, and L.Joshua-Tor (2008).
On helicases and other motor proteins.
  Curr Opin Struct Biol, 18, 243-257.  
18466635 J.Snider, G.Thibault, and W.A.Houry (2008).
The AAA+ superfamily of functionally diverse proteins.
  Genome Biol, 9, 216.  
18846282 K.Kobayashi, N.Mochizuki, N.Yoshimura, K.Motohashi, T.Hisabori, and T.Masuda (2008).
Functional analysis of Arabidopsis thaliana isoforms of the Mg-chelatase CHLI subunit.
  Photochem Photobiol Sci, 7, 1188-1195.  
18263581 N.Sirijovski, J.Lundqvist, M.Rosenbäck, H.Elmlund, S.Al-Karadaghi, R.D.Willows, and M.Hansson (2008).
Substrate-binding model of the chlorophyll biosynthetic magnesium chelatase BchH subunit.
  J Biol Chem, 283, 11652-11660.  
18273690 T.Masuda (2008).
Recent overview of the Mg branch of the tetrapyrrole biosynthesis leading to chlorophylls.
  Photosynth Res, 96, 121-143.  
18846277 T.Masuda, and Y.Fujita (2008).
Regulation and evolution of chlorophyll metabolism.
  Photochem Photobiol Sci, 7, 1131-1149.  
17123104 A.A.Apchelimov, O.P.Soldatova, T.A.Ezhova, B.Grimm, and S.V.Shestakov (2007).
The analysis of the ChlI 1 and ChlI 2 genes using acifluorfen-resistant mutant of Arabidopsis thaliana.
  Planta, 225, 935-943.  
17472958 A.Ikegami, N.Yoshimura, K.Motohashi, S.Takahashi, P.G.Romano, T.Hisabori, K.Takamiya, and T.Masuda (2007).
The CHLI1 subunit of Arabidopsis thaliana magnesium chelatase is a target protein of the chloroplast thioredoxin.
  J Biol Chem, 282, 19282-19291.  
17898893 G.L.Holliday, J.M.Thornton, A.Marquet, A.G.Smith, F.Rébeillé, R.Mendel, H.L.Schubert, A.D.Lawrence, and M.J.Warren (2007).
Evolution of enzymes and pathways for the biosynthesis of cofactors.
  Nat Prod Rep, 24, 972-987.  
17942298 J.Takagi (2007).
Structural basis for ligand recognition by integrins.
  Curr Opin Cell Biol, 19, 557-564.  
17964268 M.J.Moreau, A.T.McGeoch, A.R.Lowe, L.S.Itzhaki, and S.D.Bell (2007).
ATPase site architecture and helicase mechanism of an archaeal MCM.
  Mol Cell, 28, 304-314.  
17639347 N.Sirijovski, F.Mamedov, U.Olsson, S.Styring, and M.Hansson (2007).
Rhodobacter capsulatus magnesium chelatase subunit BchH contains an oxygen sensitive iron-sulfur cluster.
  Arch Microbiol, 188, 599-608.  
17062628 A.Costa, T.Pape, M.van Heel, P.Brick, A.Patwardhan, and S.Onesti (2006).
Structural basis of the Methanothermobacter thermautotrophicus MCM helicase activity.
  Nucleic Acids Res, 34, 5829-5838.  
16679413 E.R.Jenkinson, and J.P.Chong (2006).
Minichromosome maintenance helicase activity is controlled by N- and C-terminal motifs and requires the ATPase domain helix-2 insert.
  Proc Natl Acad Sci U S A, 103, 7613-7618.  
16915519 H.Zhang, J.Li, J.H.Yoo, S.C.Yoo, S.H.Cho, H.J.Koh, H.S.Seo, and N.C.Paek (2006).
Rice Chlorina-1 and Chlorina-9 encode ChlD and ChlI subunits of Mg-chelatase, a key enzyme for chlorophyll synthesis and chloroplast development.
  Plant Mol Biol, 62, 325-337.  
16689629 J.P.Erzberger, and J.M.Berger (2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
  Annu Rev Biophys Biomol Struct, 35, 93.  
16301313 J.Snider, I.Gutsche, M.Lin, S.Baby, B.Cox, G.Butland, J.Greenblatt, A.Emili, and W.A.Houry (2006).
Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase.
  J Biol Chem, 281, 1532-1546.  
16463102 R.J.Sawers, J.Viney, P.R.Farmer, R.R.Bussey, G.Olsefski, K.Anufrikova, C.N.Hunter, and T.P.Brutnell (2006).
The maize Oil yellow1 (Oy1) gene encodes the I subunit of magnesium chelatase.
  Plant Mol Biol, 60, 95.  
16953878 R.J.Sawers, P.R.Farmer, P.Moffett, and T.P.Brutnell (2006).
In planta transient expression as a system for genetic and biochemical analyses of chlorophyll biosynthesis.
  Plant Methods, 2, 15.  
16142223 J.P.Chong (2005).
Learning to unwind.
  Nat Struct Mol Biol, 12, 734-736.  
16128821 M.Shepherd, S.McLean, and C.N.Hunter (2005).
Kinetic basis for linking the first two enzymes of chlorophyll biosynthesis.
  FEBS J, 272, 4532-4539.  
15815918 O.Soldatova, A.Apchelimov, N.Radukina, T.Ezhova, S.Shestakov, V.Ziemann, B.Hedtke, and B.Grimm (2005).
An Arabidopsis mutant that is resistant to the protoporphyrinogen oxidase inhibitor acifluorfen shows regulatory changes in tetrapyrrole biosynthesis.
  Mol Genet Genomics, 273, 311-318.  
15051720 J.D.Reid, and C.N.Hunter (2004).
Magnesium-dependent ATPase activity and cooperativity of magnesium chelatase from Synechocystis sp. PCC6803.
  J Biol Chem, 279, 26893-26899.  
15153108 V.Lake, U.Olsson, R.D.Willows, and M.Hansson (2004).
ATPase activity of magnesium chelatase subunit I is required to maintain subunit D in vivo.
  Eur J Biochem, 271, 2182-2188.  
12686546 A.A.Brindley, E.Raux, H.K.Leech, H.L.Schubert, and M.J.Warren (2003).
A story of chelatase evolution: identification and characterization of a small 13-15-kDa "ancestral" cobaltochelatase (CbiXS) in the archaea.
  J Biol Chem, 278, 22388-22395.  
14673105 C.von Mering, E.M.Zdobnov, S.Tsoka, F.D.Ciccarelli, J.B.Pereira-Leal, C.A.Ouzounis, and P.Bork (2003).
Genome evolution reveals biochemical networks and functional modules.
  Proc Natl Acad Sci U S A, 100, 15428-15433.  
12754222 R.D.Willows, V.Lake, T.H.Roberts, and S.I.Beale (2003).
Inactivation of Mg chelatase during transition from anaerobic to aerobic growth in Rhodobacter capsulatus.
  J Bacteriol, 185, 3249-3258.  
12357035 A.Hansson, R.D.Willows, T.H.Roberts, and M.Hansson (2002).
Three semidominant barley mutants with single amino acid substitutions in the smallest magnesium chelatase subunit form defective AAA+ hexamers.
  Proc Natl Acad Sci U S A, 99, 13944-13949.  
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.  
  12102729 J.E.Garbarino, and I.R.Gibbons (2002).
Expression and genomic analysis of midasin, a novel and highly conserved AAA protein distantly related to dynein.
  BMC Genomics, 3, 18.  
12426582 K.Zeth, R.B.Ravelli, K.Paal, S.Cusack, B.Bukau, and D.A.Dougan (2002).
Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA.
  Nat Struct Biol, 9, 906-911.
PDB codes: 1lzw 1mg9
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.