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PDBsum entry 1cz5

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Hydrolase PDB id
1cz5
Jmol
Contents
Protein chain
185 a.a. *
* Residue conservation analysis
PDB id:
1cz5
Name: Hydrolase
Title: Nmr structure of vat-n: the n-terminal domain of vat (vcp- like atpase of thermoplasma)
Structure: Vcp-like atpase. Chain: a. Fragment: n-terminal domain: m1 to e183 followed by a diglycine spacer. Engineered: yes
Source: Thermoplasma acidophilum. Organism_taxid: 2303. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 25 models
Authors: M.Coles,T.Diercks,J.Liermann,A.Groeger,B.Rockel, W.Baumeister,K.Koretke,A.Lupas,J.Peters,H.Kessler
Key ref:
M.Coles et al. (1999). The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. Curr Biol, 9, 1158-1168. PubMed id: 10531028 DOI: 10.1016/S0960-9822(00)80017-2
Date:
01-Sep-99     Release date:   12-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O05209  (VAT_THEAC) -  VCP-like ATPase
Seq:
Struc:
 
Seq:
Struc:
745 a.a.
185 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
DOI no: 10.1016/S0960-9822(00)80017-2 Curr Biol 9:1158-1168 (1999)
PubMed id: 10531028  
 
 
The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element.
M.Coles, T.Diercks, J.Liermann, A.Gröger, B.Rockel, W.Baumeister, K.K.Koretke, A.Lupas, J.Peters, H.Kessler.
 
  ABSTRACT  
 
BACKGROUND: The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. RESULTS: Using nuclear magnetic resonance (NMR) spectroscopy, we found that VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn (comprising residues Met1-Thr92) forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc (comprising residues Glu93-Gly185) forms a novel six-stranded beta-clam fold. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. Sequence and structure analyses showed that VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. These proteins map out an evolutionary path from simple homodimeric transcription factors containing a single copy of the VAT-Nn repeat to complex enzymes containing four copies. CONCLUSIONS: Our results suggest that VAT-N is a precursor of the aspartic proteinases that has acquired peptide-binding activity while remaining proteolytically incompetent. We propose that the binding site of the protein is similar to that of aspartic proteinases, in that it lies between the psi-loops of the amino-terminal beta-barrel and that it coincides with a crescent-shaped band of positive charge extending across the upper face of the molecule.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Folding topology of VAT-N. The characteristic H^α–H^α and H^N–H^N NOE connectivities used to determine the arrangement of β-strands are shown (black and white arrows, respectively). The data show β bulges in strands β7 and β10. Loops indicated by dashed lines are not to scale. The psi-loops in the amino-terminal subdomain are in bold. N, amino terminus; C, carboxyl terminus.
Figure 6.
Figure 6. GRASP [32] and [33] surface of VAT-N. Two views are shown; the left panels are equivalent to those shown in Figure 4, that is, looking at the top of the hexameric ring, whereas the right panels represent a view looking from within the ring towards the cleft between the two subdomains. The upper panels are coloured according to electrostatic potential, with values ranging from −7.0 (red) to 7.0 (blue) in units of k[B]T, and bottom panels according to the hydrophobicity of the underlying residues (hydrophobic, polar, positively charged and negatively charged residues are shown in white, green, blue and red, respectively). The strong positive charge of the top surface of the molecule is evident. This is mainly due to the many arginine residues concentrated on this face of the protein. In contrast, the inner surface of the protein is relatively uncharged or negatively charged.
 
  The above figures are reprinted by permission from Cell Press: Curr Biol (1999, 9, 1158-1168) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20525292 C.Kim, J.Basner, and B.Lee (2010).
Detecting internally symmetric protein structures.
  BMC Bioinformatics, 11, 303.  
20135044 J.L.Barneto, M.Avalos, R.Babiano, P.Cintas, J.L.Jiménez, and J.C.Palacios (2010).
A new model for mapping the peptide backbone: predicting proton chemical shifts in proteins.
  Org Biomol Chem, 8, 857-863.  
19609930 V.Alva, S.Dunin-Horkawicz, M.Habeck, M.Coles, and A.N.Lupas (2009).
The GD box: a widespread noncontiguous supersecondary structural element.
  Protein Sci, 18, 1961-1966.  
17979191 I.Chaudhuri, J.Söding, and A.N.Lupas (2008).
Evolution of the beta-propeller fold.
  Proteins, 71, 795-803.  
18457946 V.Alva, K.K.Koretke, M.Coles, and A.N.Lupas (2008).
Cradle-loop barrels and the concept of metafolds in protein classification by natural descent.
  Curr Opin Struct Biol, 18, 358-365.  
18073108 M.Ammelburg, M.D.Hartmann, S.Djuranovic, V.Alva, K.K.Koretke, J.Martin, G.Sauer, V.Truffault, K.Zeth, A.N.Lupas, and M.Coles (2007).
A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.
  Structure, 15, 1577-1590.
PDB codes: 2p3m 2vbs 2vbt 2vbu 2vbv
17384229 M.Hulko, A.N.Lupas, and J.Martin (2007).
Inherent chaperone-like activity of aspartic proteases reveals a distant evolutionary relation to double-psi barrel domains of AAA-ATPases.
  Protein Sci, 16, 644-653.  
17706670 O.Schmidt, V.J.Schuenemann, N.J.Hand, T.J.Silhavy, J.Martin, A.N.Lupas, and S.Djuranovic (2007).
prlF and yhaV encode a new toxin-antitoxin system in Escherichia coli.
  J Mol Biol, 372, 894-905.  
17715145 S.Balaji, and L.Aravind (2007).
The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins.
  Nucleic Acids Res, 35, 5658-5671.  
17899394 S.W.Ginzinger, F.Gerick, M.Coles, and V.Heun (2007).
CheckShift: automatic correction of inconsistent chemical shift referencing.
  J Biomol NMR, 39, 223-227.  
17202270 V.E.Pye, F.Beuron, C.A.Keetch, C.McKeown, C.V.Robinson, H.H.Meyer, X.Zhang, and P.S.Freemont (2007).
Structural insights into the p97-Ufd1-Npl4 complex.
  Proc Natl Acad Sci U S A, 104, 467-472.  
16373473 J.H.Brown (2006).
Breaking symmetry in protein dimers: designs and functions.
  Protein Sci, 15, 1.  
17018057 K.Shiozawa, N.Goda, T.Shimizu, K.Mizuguchi, N.Kondo, N.Shimozawa, M.Shirakawa, and H.Hiroaki (2006).
The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97.
  FEBS J, 273, 4959-4971.  
17027498 M.Coles, M.Hulko, S.Djuranovic, V.Truffault, K.Koretke, J.Martin, and A.N.Lupas (2006).
Common evolutionary origin of swapped-hairpin and double-psi beta barrels.
  Structure, 14, 1489-1498.
PDB code: 2glw
16826545 M.V.Deshmukh, M.John, M.Coles, J.Peters, W.Baumeister, and H.Kessler (2006).
Inter-domain orientation and motions in VAT-N explored by residual dipolar couplings and 15N backbone relaxation.
  Magn Reson Chem, 44, S89.  
16236712 A.Gerega, B.Rockel, J.Peters, T.Tamura, W.Baumeister, and P.Zwickl (2005).
VAT, the thermoplasma homolog of mammalian p97/VCP, is an N domain-regulated protein unfoldase.
  J Biol Chem, 280, 42856-42862.  
15939023 M.Coles, S.Djuranovic, J.Söding, T.Frickey, K.Koretke, V.Truffault, J.Martin, and A.N.Lupas (2005).
AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels.
  Structure, 13, 919-928.
PDB codes: 1yfb 1ysf
14988733 I.Dreveny, H.Kondo, K.Uchiyama, A.Shaw, X.Zhang, and P.S.Freemont (2004).
Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47.
  EMBO J, 23, 1030-1039.
PDB code: 1s3s
15371428 R.M.Bruderer, C.Brasseur, and H.H.Meyer (2004).
The AAA ATPase p97/VCP interacts with its alternative co-factors, Ufd1-Npl4 and p47, through a common bipartite binding mechanism.
  J Biol Chem, 279, 49609-49616.  
15281131 V.Anantharaman, and L.Aravind (2004).
The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies.
  Proteins, 56, 795-807.  
12949490 B.DeLaBarre, and A.T.Brunger (2003).
Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains.
  Nat Struct Biol, 10, 856-863.
PDB code: 1oz4
12937274 J.J.Partridge, J.O.Lopreiato, M.Latterich, and F.E.Indig (2003).
DNA damage modulates nucleolar interaction of the Werner protein with the AAA ATPase p97/VCP.
  Mol Biol Cell, 14, 4221-4229.  
12553882 L.M.Iyer, E.V.Koonin, and L.Aravind (2003).
Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases.
  BMC Struct Biol, 3, 1.  
14594825 N.J.Hand, and T.J.Silhavy (2003).
Null mutations in a Nudix gene, ygdP, implicate an alarmone response in a novel suppression of hybrid jamming.
  J Bacteriol, 185, 6530-6539.  
12847084 Y.Ye, H.H.Meyer, and T.A.Rapoport (2003).
Function of the p97-Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains.
  J Cell Biol, 162, 71-84.  
12434150 I.Rouiller, B.DeLaBarre, A.P.May, W.I.Weis, A.T.Brunger, R.A.Milligan, and E.M.Wilson-Kubalek (2002).
Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle.
  Nat Struct Biol, 9, 950-957.  
12021456 K.K.Koretke, R.B.Russell, and A.N.Lupas (2002).
Fold recognition without folds.
  Protein Sci, 11, 1575-1579.  
11340056 A.T.Brunger (2001).
Structure of proteins involved in synaptic vesicle fusion in neurons.
  Annu Rev Biophys Biomol Struct, 30, 157-171.  
11297924 A.T.Brunger (2001).
Structural insights into the molecular mechanism of calcium-dependent vesicle-membrane fusion.
  Curr Opin Struct Biol, 11, 163-173.  
11835483 K.K.Koretke, R.B.Russell, and A.N.Lupas (2001).
Fold recognition from sequence comparisons.
  Proteins, (), 68-75.  
11473577 T.Ogura, and A.J.Wilkinson (2001).
AAA+ superfamily ATPases: common structure--diverse function.
  Genes Cells, 6, 575-597.  
10851178 A.T.Brunger (2000).
Structural insights into the molecular mechanism of Ca(2+)-dependent exocytosis.
  Curr Opin Neurobiol, 10, 293-302.  
10811609 H.H.Meyer, J.G.Shorter, J.Seemann, D.Pappin, and G.Warren (2000).
A complex of mammalian ufd1 and npl4 links the AAA-ATPase, p97, to ubiquitin and nuclear transport pathways.
  EMBO J, 19, 2181-2192.  
11163219 X.Zhang, A.Shaw, P.A.Bates, R.H.Newman, B.Gowen, E.Orlova, M.A.Gorman, H.Kondo, P.Dokurno, J.Lally, G.Leonard, H.Meyer, M.van Heel, and P.S.Freemont (2000).
Structure of the AAA ATPase p97.
  Mol Cell, 6, 1473-1484.
PDB code: 1e32
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.