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PDBsum entry 1hux
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Metal binding protein PDB id
1hux

 

 

 

 

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Contents
Protein chains
259 a.a. *
Ligands
SF4
ADP ×2
* Residue conservation analysis
PDB id:
1hux
Name: Metal binding protein
Title: Crystal structure of the acidaminococcus fermentans (r)-2- hydroxyglutaryl-coa dehydratase component a
Structure: Activator of (r)-2-hydroxyglutaryl-coa dehydratase. Chain: a, b. Engineered: yes
Source: Acidaminococcus fermentans. Organism_taxid: 905. Gene: hgdc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
3.00Å     R-factor:   0.236     R-free:   0.279
Authors: K.P.Locher,M.Hans,A.P.Yeh,B.Schmid,W.Buckel,D.C.Rees
Key ref:
K.P.Locher et al. (2001). Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A. J Mol Biol, 307, 297-308. PubMed id: 11243821 DOI: 10.1006/jmbi.2000.4496
Date:
04-Jan-01     Release date:   21-Mar-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P11568  (HGDC_ACIFV) -  (R)-2-hydroxyglutaryl-CoA dehydratase activating ATPase from Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4)
Seq:
Struc: 		260 a.a.
259 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.1.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1006/jmbi.2000.4496 J Mol Biol 307:297-308 (2001)
PubMed id: 11243821  
 
 
Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A.
K.P.Locher, M.Hans, A.P.Yeh, B.Schmid, W.Buckel, D.C.Rees.
 
  ABSTRACT  
 
Acidaminococcus fermentans degrades glutamate via the hydroxyglutarate pathway, which involves the syn-elimination of water from (R)-2-hydroxyglutaryl-CoA in a key reaction of the pathway. This anaerobic process is catalyzed by 2-hydroxyglutaryl-CoA dehydratase, an enzyme with two components (A and D) that reversibly associate during reaction cycles. Component A (CompA), a homodimeric cluster and uses the hydrolysis of ATP to deliver an electron to the dehydratase component (CompD), where the electron is used catalytically. The structure of the extremely oxygen-sensitive CompA protein was solved by X-ray crystallography to 3 A resolution. The protein was found to be a member of the actin fold family, revealing a similar architecture and nucleotide-binding site. The key differences between CompA and other members of the actin fold family are: (i) the presence of a cluster binding segment, the "cluster helix"; (ii) cluster; and (iii) the location of the homodimer interface, which involves the bridging cluster. Possible reaction mechanisms are discussed in light of the close structural similarity to members of the actin-fold family and the functional similarity to the nitrogenase Fe- protein.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Superposition of CompA (monomer A) and hsc70 (PDB entry 3HSC). A stereo view of a ribbon representation is shown, with CompA and Hsc70 in purple and yellow, respectively. The [4Fe-4S] cluster is shown as a CPK model, with sulfur and iron in green and red. The superposition of these structures was performed using 182 C^a atoms with a r.m.s. deviation of 2.3 Å. The following segments were superimposed: CompA (Hsc70) 4-21 (5-22), 31-37 (37-43), 39-56 (122-139), 61-66 (141-146), 71-74 (161-164), 76-89 (169-182), 90-93 (180-183), 98-115 (195-212), 118-125 (219-226), 131-141 (229-239), 145-150 (270-275), 186-190 (300-304), 194-207 (308-321), 209-235 (331-357), 236-239 (359-362), 241-258 (364-381). 		Figure 3.
Figure 3. Stereoviews of the homodimeric CompA protein. Ribbon representations are shown from "top" and "side" views, with monomer A in green and cyan and monomer B in purple and dark red. ADP is shown in ball-and-stick, and the [4Fe-4S] cluster is shown as a CPK model (red and yellow spheres for iron and sulfur, respectively). The top view is along the non-crystallographic 2-fold symmetry axis, whereas the side view is turned by 90° to the left, with the 2-fold lying horizontally in the plane of the paper. The molecule was additionally rotated a few degrees around the 2-fold axis in this view. The bottom view is shown in CPK representation, with the four sulfur atoms of the cluster shown in green.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 297-308) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20146278 J.Kim, A.J.Pierik, and W.Buckel (2010).
A complex of 2-hydroxyisocaproyl-coenzyme A dehydratase and its activator from Clostridium difficile stabilized by aluminium tetrafluoride-adenosine diphosphate.
  Chemphyschem, 11, 1307-1312.  
18096851 L.L.Grochowski, and R.H.White (2008).
Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea.
  Ann N Y Acad Sci, 1125, 190-214.  
18274792 M.Hans, W.Buckel, and E.Bill (2008).
Spectroscopic evidence for an all-ferrous [4Fe-4S]0 cluster in the superreduced activator of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans.
  J Biol Inorg Chem, 13, 563-574.  
17766251 A.Hecker, N.Leulliot, D.Gadelle, M.Graille, A.Justome, P.Dorlet, C.Brochier, S.Quevillon-Cheruel, E.Le Cam, H.van Tilbeurgh, and P.Forterre (2007).
An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro.
  Nucleic Acids Res, 35, 6042-6051.
PDB codes: 2ivn 2ivo 2ivp
17578578 J.E.Butler, Q.He, K.P.Nevin, Z.He, J.Zhou, and D.R.Lovley (2007).
Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site.
  BMC Genomics, 8, 180.  
17457690 M.Heinnickel, and J.H.Golbeck (2007).
Heliobacterial photosynthesis.
  Photosynth Res, 92, 35-53.  
16905100 J.Alvarado, A.Ghosh, T.Janovitz, A.Jauregui, M.S.Hasson, and D.A.Sanders (2006).
Origin of exopolyphosphatase processivity: Fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog.
  Structure, 14, 1263-1272.
PDB code: 1u6z
16855243 K.Yang, Y.Eyobo, L.A.Brand, D.Martynowski, D.Tomchick, E.Strauss, and H.Zhang (2006).
Crystal structure of a type III pantothenate kinase: insight into the mechanism of an essential coenzyme A biosynthetic enzyme universally distributed in bacteria.
  J Bacteriol, 188, 5532-5540.
PDB code: 2gtd
16704345 W.Buckel, and B.T.Golding (2006).
Radical enzymes in anaerobes.
  Annu Rev Microbiol, 60, 27-49.  
15812036 B.Song, and B.B.Ward (2005).
Genetic diversity of benzoyl coenzyme A reductase genes detected in denitrifying isolates and estuarine sediment communities.
  Appl Environ Microbiol, 71, 2036-2045.  
15654892 J.Kim, D.Darley, and W.Buckel (2005).
2-Hydroxyisocaproyl-CoA dehydratase and its activator from Clostridium difficile.
  FEBS J, 272, 550-561.  
15771780 S.Cheek, K.Ginalski, H.Zhang, and N.V.Grishin (2005).
A comprehensive update of the sequence and structure classification of kinases.
  BMC Struct Biol, 5, 6.  
16218867 W.Buckel, B.M.Martins, A.Messerschmidt, and B.T.Golding (2005).
Radical-mediated dehydration reactions in anaerobic bacteria.
  Biol Chem, 386, 951-959.  
  15374661 J.Kim, M.Hetzel, C.D.Boiangiu, and W.Buckel (2004).
Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of alpha-amino acids by anaerobic bacteria.
  FEMS Microbiol Rev, 28, 455-468.  
15263897 R.Dixon, and D.Kahn (2004).
Genetic regulation of biological nitrogen fixation.
  Nat Rev Microbiol, 2, 621-631.  
12413544 M.Boll, G.Fuchs, and J.Heider (2002).
Anaerobic oxidation of aromatic compounds and hydrocarbons.
  Curr Opin Chem Biol, 6, 604-611.  
11856823 M.H.Bucher, A.G.Evdokimov, and D.S.Waugh (2002).
Differential effects of short affinity tags on the crystallization of Pyrococcus furiosus maltodextrin-binding protein.
  Acta Crystallogr D Biol Crystallogr, 58, 392-397.  
11980491 M.Hans, E.Bill, I.Cirpus, A.J.Pierik, M.Hetzel, D.Alber, and W.Buckel (2002).
Adenosine triphosphate-induced electron transfer in 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans.
  Biochemistry, 41, 5873-5882.  
11967068 S.Dickert, A.J.Pierik, and W.Buckel (2002).
Molecular characterization of phenyllactate dehydratase and its initiator from Clostridium sporogenes.
  Mol Microbiol, 44, 49-60.  
11959504 W.Saenger, P.Jordan, and N.Krauss (2002).
The assembly of protein subunits and cofactors in photosystem I.
  Curr Opin Struct Biol, 12, 244-254.  
11698658 M.Unciuleac, and M.Boll (2001).
Mechanism of ATP-driven electron transfer catalyzed by the benzene ring-reducing enzyme benzoyl-CoA reductase.
  Proc Natl Acad Sci U S A, 98, 13619-13624.  
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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