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PDBsum entry 1g20
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1g20

 

 

 

 

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Contents
Protein chains
476 a.a. *
522 a.a. *
259 a.a. *
Ligands
HCA ×2
CFM ×2
CLF ×2
SF4 ×2
Metals
_CA ×2
Waters ×1066
* Residue conservation analysis
PDB id:
1g20
Name: Oxidoreductase
Title: Mgatp-bound and nucleotide-free structures of a nitrogenase protein complex between leu127del-fe protein and the mofe protein
Structure: Nitrogenase molybdenum-iron protein alpha chain. Chain: a, c. Synonym: nitrogenase component i, dinitrogenase, nifd. Nitrogenase molybdenum-iron protein beta chain. Chain: b, d. Synonym: nitrogenase component i, dinitrogenase, nifk. Nitrogenase iron protein. Chain: e, f, g, h. Synonym: nitrogenase component ii, nitrogenase reductase, nifh.
Source: Azotobacter vinelandii. Organism_taxid: 354. Organism_taxid: 354
Biol. unit: Octamer (from PQS)
Resolution:
2.20Å     R-factor:   0.219     R-free:   0.255
Authors: H.-J.Chiu,J.W.Peters,W.N.Lanzilotta,M.J.Ryle,L.C.Seefeldt,J.B.Howard, D.C.Rees
Key ref:
H.Chiu et al. (2001). MgATP-Bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127 Delta-Fe-protein and the MoFe-protein. Biochemistry, 40, 641-650. PubMed id: 11170380 DOI: 10.1021/bi001645e
Date:
16-Oct-00     Release date:   31-Jan-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07328  (NIFD_AZOVI) -  Nitrogenase molybdenum-iron protein alpha chain from Azotobacter vinelandii
Seq:
Struc: 		492 a.a.
476 a.a.
Protein chains
Pfam   ArchSchema ?
P07329  (NIFK_AZOVI) -  Nitrogenase molybdenum-iron protein beta chain from Azotobacter vinelandii
Seq:
Struc: 		 
Seq:
Struc: 		523 a.a.
522 a.a.
Protein chains
Pfam   ArchSchema ?
P00459  (NIFH1_AZOVI) -  Nitrogenase iron protein 1 from Azotobacter vinelandii
Seq:
Struc: 		290 a.a.
259 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.1.18.6.1  - nitrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Nitrogenase
      Reaction: N2 + 8 reduced [2Fe-2S]-[ferredoxin] + 16 ATP + 16 H2O = H2 + 8 oxidized [2Fe-2S]-[ferredoxin] + 2 NH4+ + 16 ADP + 16 phosphate + 6 H+
N2
 + 8 × reduced [2Fe-2S]-[ferredoxin]
 + 16 × ATP
 + 16 × H2O
 = H2
 + 8 × oxidized [2Fe-2S]-[ferredoxin]
 + 2 × NH4(+)
 + 16 × ADP
 + 16 × phosphate
 + 6 × H(+)
      Cofactor: Iron-sulfur; Vanadium cation or Mo cation
Iron-sulfur
 Vanadium cation
 or Mo cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/bi001645e Biochemistry 40:641-650 (2001)
PubMed id: 11170380  
 
 
MgATP-Bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127 Delta-Fe-protein and the MoFe-protein.
H.Chiu, J.W.Peters, W.N.Lanzilotta, M.J.Ryle, L.C.Seefeldt, J.B.Howard, D.C.Rees.
 
  ABSTRACT  
 
A mutant form of the nitrogenase iron protein with a deletion of residue Leu 127, located in the switch II region of the nucleotide binding site, forms a tight, inactive complex with the nitrogenase molybdenum iron (MoFe) protein in the absence of nucleotide. The structure of this complex generated with proteins from Azotobacter vinelandii (designated the L127Delta-Av2-Av1 complex) has been crystallographically determined in the absence of nucleotide at 2.2 A resolution and with bound MgATP (introduced by soaking) at 3.0 A resolution. As observed in the structure of the complex between the wild-type A. vinelandii nitrogenase proteins stabilized with ADP.AlF(4-), the most significant conformational changes in the L127Delta complex occur in the Fe-protein component. While the interactions at the interface between the MoFe-protein and Fe-proteins are conserved in the two complexes, significant differences are evident at the subunit-subunit interface of the dimeric Fe-proteins, with the L127Delta-Av2 structure having a more open conformation than the wild-type Av2 in the complex stabilized by ADP.AlF(4-). Addition of MgATP to the L127Delta-Av2-Av1 complex results in a further increase in the separation between Fe-protein subunits so that the structure more closely resembles that of the wild-type, nucleotide-free, uncomplexed Fe-protein, rather than the Fe-protein conformation in the ADP.AlF(4-) complex. The L127Delta mutation precludes key interactions between the Fe-protein and nucleotide, especially, but not exclusively, in the region corresponding to the switch II region of G-proteins, where the deletion constrains Gly 128 and Asp 129 from forming hydrogen bonds to the gamma-phosphate and activating water for attack on this group, respectively. These alterations account for the inability of this mutant to support mechanistically productive ATP hydrolysis. The ability of the L127Delta-Av2-Av1 complex to bind MgATP demonstrates that dissociation of the nitrogenase complex is not required for nucleotide binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20498089 E.M.Shepard, S.E.McGlynn, A.L.Bueling, C.S.Grady-Smith, S.J.George, M.A.Winslow, S.P.Cramer, J.W.Peters, and J.B.Broderick (2010).
Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold.
  Proc Natl Acad Sci U S A, 107, 10448-10453.  
21210973 L.M.Lery, M.Bitar, M.G.Costa, S.C.Rössle, and P.M.Bisch (2010).
Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria.
  BMC Genomics, 11, S7.  
20075073 M.J.Bröcker, D.Wätzlich, M.Saggu, F.Lendzian, J.Moser, and D.Jahn (2010).
Biosynthesis of (bacterio)chlorophylls: ATP-dependent transient subunit interaction and electron transfer of dark operative protochlorophyllide oxidoreductase.
  J Biol Chem, 285, 8268-8277.  
19336405 D.Wätzlich, M.J.Bröcker, F.Uliczka, M.Ribbe, S.Virus, D.Jahn, and J.Moser (2009).
Chimeric nitrogenase-like enzymes of (bacterio)chlorophyll biosynthesis.
  J Biol Chem, 284, 15530-15540.  
19489731 L.C.Seefeldt, B.M.Hoffman, and D.R.Dean (2009).
Mechanism of Mo-dependent nitrogenase.
  Annu Rev Biochem, 78, 701-722.  
19234722 P.C.Hallenbeck, G.N.George, R.C.Prince, and R.N.Thorneley (2009).
Characterization of a modified nitrogenase Fe protein from Klebsiella pneumoniae in which the 4Fe4S cluster has been replaced by a 4Fe4Se cluster.
  J Biol Inorg Chem, 14, 673-682.  
18386081 J.Petersen, C.J.Mitchell, K.Fisher, and D.J.Lowe (2008).
Structural basis for VO(2+)-inhibition of nitrogenase activity: (B) pH-sensitive inner-sphere rearrangements in the 1H-environment of the metal coordination site of the nitrogenase Fe-protein identified by ENDOR spectroscopy.
  J Biol Inorg Chem, 13, 637-650.  
16688314 B.M.Barney, H.I.Lee, P.C.Dos Santos, B.M.Hoffman, D.R.Dean, and L.C.Seefeldt (2006).
Breaking the N2 triple bond: insights into the nitrogenase mechanism.
  Dalton Trans, (), 2277-2284.  
17088547 J.B.Howard, and D.C.Rees (2006).
How many metals does it take to fix N2? A mechanistic overview of biological nitrogen fixation.
  Proc Natl Acad Sci U S A, 103, 17088-17093.  
16510305 J.W.Peters, and R.K.Szilagyi (2006).
Exploring new frontiers of nitrogenase structure and mechanism.
  Curr Opin Chem Biol, 10, 101-108.  
16315272 S.Sen, and J.W.Peters (2006).
The thermal adaptation of the nitrogenase Fe protein from thermophilic Methanobacter thermoautotrophicus.
  Proteins, 62, 450-460.  
16123301 F.A.Tezcan, J.T.Kaiser, D.Mustafi, M.Y.Walton, J.B.Howard, and D.C.Rees (2005).
Nitrogenase complexes: multiple docking sites for a nucleotide switch protein.
  Science, 309, 1377-1380.
PDB codes: 2afh 2afi 2afk 4wzb
12045096 D.C.Rees (2002).
Great metalloclusters in enzymology.
  Annu Rev Biochem, 71, 221-246.  
12403627 J.Petersen, K.Fisher, C.J.Mitchell, and D.J.Lowe (2002).
Multiple inequivalent metal-nucleotide coordination environments in the presence of the VO2+-inhibited nitrogenase iron protein: pH-dependent structural rearrangements at the nucleotide binding site.
  Biochemistry, 41, 13253-13263.  
12475211 V.L.Davidson (2002).
Chemically gated electron transfer. A means of accelerating and regulating rates of biological electron transfer.
  Biochemistry, 41, 14633-14636.  
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.

 

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