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PDBsum entry 1fc9

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protein links
Hydrolase PDB id
1fc9
Jmol
Contents
Protein chain
386 a.a. *
Waters ×212
* Residue conservation analysis
PDB id:
1fc9
Name: Hydrolase
Title: Photosystem ii d1 c-terminal processing protease
Structure: Photosystem ii d1 protease. Chain: a. Fragment: residues 77-464. Synonym: d1 c-terminal processing protease. Engineered: yes
Source: Scenedesmus obliquus. Organism_taxid: 3088. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.191     R-free:   0.275
Authors: D.I.Liao,J.Qian,D.A.Chisholm,D.B.Jordan,B.A.Diner
Key ref:
D.I.Liao et al. (2000). Crystal structures of the photosystem II D1 C-terminal processing protease. Nat Struct Biol, 7, 749-753. PubMed id: 10966643 DOI: 10.1038/78973
Date:
18-Jul-00     Release date:   18-Jan-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O04073  (O04073_SCEOB) -  C-terminal processing peptidase, chloroplastic
Seq:
Struc:
464 a.a.
386 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.102  - C-terminal processing peptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: The enzyme shows specific recognition of a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr, and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. A typical cleavage is -Ala-Ala-|-Arg-Ala-Ala-Lys-Glu-Asn-Tyr-Ala-Leu-Ala-Ala. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     serine-type peptidase activity     1 term  

 

 
DOI no: 10.1038/78973 Nat Struct Biol 7:749-753 (2000)
PubMed id: 10966643  
 
 
Crystal structures of the photosystem II D1 C-terminal processing protease.
D.I.Liao, J.Qian, D.A.Chisholm, D.B.Jordan, B.A.Diner.
 
  ABSTRACT  
 
We report here the first three-dimensional structure of the D1 C-terminal processing protease (D1P), which is encoded by the ctpA gene. This enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II of oxygenic photosynthesis. Proteolytic processing is necessary to allow the light driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation. The X-ray structure of the Scenedesmus obliquus enzyme has been determined at 1.8 A resolution using the multiwavelength anomalous dispersion method. The enzyme is monomeric and is composed of three folding domains. The middle domain is topologically homologous to known PDZ motifs and is proposed to be the site at which the substrate C-terminus binds. The remainder of the substrate likely extends across the face of the enzyme, interacting at its scissile bond with the enzyme active site Ser 372 / Lys 397 catalytic dyad, which lies at the center of the protein at the interface of the three domains.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of D1 protease. a, Ribbon drawing of D1P. The A domain is in red, the B domain in yellow and the C domain in blue. The extended -hairpin loop from the C domain forms an integral part of the folding domain A and is regarded as part of that domain. The loops that connect domains A to B and B to C have very high temperature factors and are colored in green. The side chains of the residues involved in catalysis or substrate binding, K397, S372 and R247, are shown in ball-and-stick representation. The GVGL loop in the B domain, highlighted in magenta, has been shown to be involved in the binding of the C-terminal residues of the peptide ligand in the structurally homologous third PDZ domain of synaptic protein PSD-95^25. b, Stereo view of the C trace of D1P. Every 10^th residue and the N-terminus and C-terminus are labeled. The disulfide bond between Cys 260 and Cys 451 is shown in yellow. The orientation of the molecule is the same as the standard orientation in (a).
Figure 4.
Figure 4. The PDZ domain. a, Schematic diagram of the secondary structures of the B domain of D1P (upper) and the third PDZ domain of human D1gA (PDB accession code 1PDR, residues 463 -544)24, the third PDZ domain of the synaptic protein PSD-95 (1KWA, residues 487 -570)25 and the PDZ domain of neuronal nitric oxide synthase (1QAU, residues 14 -101)26. The location of the conserved Arg/Lys (Arg 247 in D1P, Arg 471 in 1PDR, Lys 495 in 1KWA and Arg 23 in 1QAU) is marked by a red circle. The location of the GLGF repeat of the carboxylate binding loop in 1PDR and 1QAU (GVGL in D1P and PMGL in 1KWA) is labeled by a yellow circle. Their three-dimensional structures are also very similar. The r.m.s.d. for C atoms between D1P and 1PDR is 1.5 using 76 matching residues for the alignment. The r.m.s.d. is 1.79 for 81 matching pairs of C atoms between D1P and 1QAU. For D1P and 1KWA, the r.m.s.d. is 1.9 for 71 matching pairs. b, The conserved Arg 247 in the B domain of D1P. The side chain of Arg 247 is partially buried with a solvent accessible area of 23 2.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 749-753) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21283644 A.J.Te Velthuis, P.A.Sakalis, D.A.Fowler, and C.P.Bagowski (2011).
Genome-Wide Analysis of PDZ Domain Binding Reveals Inherent Functional Overlap within the PDZ Interaction Network.
  PLoS One, 6, e16047.  
20398246 M.Münz, R.Lyngsø, J.Hein, and P.C.Biggin (2010).
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity.
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21076399 S.Gianni, Y.Ivarsson, A.De Simone, C.Travaglini-Allocatelli, M.Brunori, and M.Vendruscolo (2010).
Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain.
  Nat Struct Mol Biol, 17, 1431-1437.  
19388144 D.Chen, J.Chai, P.J.Hart, and G.Zhong (2009).
Identifying catalytic residues in CPAF, a Chlamydia-secreted protease.
  Arch Biochem Biophys, 485, 16-23.  
19654317 D.Kress, D.Brügel, I.Schall, D.Linder, W.Buckel, and L.O.Essen (2009).
An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases.
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PDB codes: 3gf3 3gf7 3glm 3gma
19273681 Z.Sun, J.Zhong, X.Liang, J.Liu, X.Chen, and L.Huan (2009).
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  Antimicrob Agents Chemother, 53, 1964-1973.  
18321962 D.J.Müller, N.Wu, and K.Palczewski (2008).
Vertebrate membrane proteins: structure, function, and insights from biophysical approaches.
  Pharmacol Rev, 60, 43-78.  
18824507 O.D.Ekici, M.Paetzel, and R.E.Dalbey (2008).
Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration.
  Protein Sci, 17, 2023-2037.  
18263589 Y.Ivarsson, C.Travaglini-Allocatelli, M.Brunori, and S.Gianni (2008).
Folding and misfolding in a naturally occurring circularly permuted PDZ domain.
  J Biol Chem, 283, 8954-8960.  
  19064254 Z.Huang, Y.Feng, D.Chen, X.Wu, S.Huang, X.Wang, X.Xiao, W.Li, N.Huang, L.Gu, G.Zhong, and J.Chai (2008).
Structural basis for activation and inhibition of the secreted chlamydia protease CPAF.
  Cell Host Microbe, 4, 529-542.
PDB codes: 3dja 3dor 3dpm 3dpn
17983264 C.H.Yeang, and D.Haussler (2007).
Detecting coevolution in and among protein domains.
  PLoS Comput Biol, 3, e211.  
17277057 J.Iwanczyk, D.Damjanovic, J.Kooistra, V.Leong, A.Jomaa, R.Ghirlando, and J.Ortega (2007).
Role of the PDZ domains in Escherichia coli DegP protein.
  J Bacteriol, 189, 3176-3186.  
17551844 K.Satoh, and Y.Yamamoto (2007).
The carboxyl-terminal processing of precursor D1 protein of the photosystem II reaction center.
  Photosynth Res, 94, 203-215.  
17631635 S.P.Lad, G.Yang, D.A.Scott, G.Wang, P.Nair, J.Mathison, V.S.Reddy, and E.Li (2007).
Chlamydial CT441 is a PDZ domain-containing tail-specific protease that interferes with the NF-kappaB pathway of immune response.
  J Bacteriol, 189, 6619-6625.  
  16582483 J.Lee, A.R.Feldman, B.Delmas, and M.Paetzel (2006).
Expression, purification and crystallization of a birnavirus-encoded protease, VP4, from blotched snakehead virus (BSNV).
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  17200656 J.M.Nickerson, R.A.Frey, V.T.Ciavatta, and D.L.Stenkamp (2006).
Interphotoreceptor retinoid-binding protein gene structure in tetrapods and teleost fish.
  Mol Vis, 12, 1565-1585.  
16895613 L.P.Tripathi, and R.Sowdhamini (2006).
Cross genome comparisons of serine proteases in Arabidopsis and rice.
  BMC Genomics, 7, 200.  
16669775 W.Sakamoto (2006).
Protein degradation machineries in plastids.
  Annu Rev Plant Biol, 57, 599-621.  
15726567 B.J.Fabbri, S.M.Duff, E.E.Remsen, Y.C.Chen, J.C.Anderson, and C.A.CaJacob (2005).
The carboxyterminal processing protease of D1 protein: expression, purification and enzymology of the recombinant and native spinach proteins.
  Pest Manag Sci, 61, 682-690.  
15678420 M.Groll, M.Bochtler, H.Brandstetter, T.Clausen, and R.Huber (2005).
Molecular machines for protein degradation.
  Chembiochem, 6, 222-256.  
15137941 C.Wilken, K.Kitzing, R.Kurzbauer, M.Ehrmann, and T.Clausen (2004).
Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease.
  Cell, 117, 483-494.
PDB codes: 1sot 1soz 1vcw
15028692 Y.Ostberg, J.A.Carroll, M.Pinne, J.G.Krum, P.Rosa, and S.Bergström (2004).
Pleiotropic effects of inactivating a carboxyl-terminal protease, CtpA, in Borrelia burgdorferi.
  J Bacteriol, 186, 2074-2084.  
14526016 Q.Pan, R.Losick, and D.Z.Rudner (2003).
A second PDZ-containing serine protease contributes to activation of the sporulation transcription factor sigmaK in Bacillus subtilis.
  J Bacteriol, 185, 6051-6056.  
14612247 T.Jansèn, H.Kidron, A.Soitamo, T.Salminen, and P.Mäenpää (2003).
Transcriptional regulation and structural modelling of the Synechocystis sp. PCC 6803 carboxyl-terminal endoprotease family.
  FEMS Microbiol Lett, 228, 121-128.  
11796109 A.Loew, and F.Gonzalez-Fernandez (2002).
Crystal structure of the functional unit of interphotoreceptor retinoid binding protein.
  Structure, 10, 43-49.
PDB code: 1j7x
12177052 A.Spiers, H.K.Lamb, S.Cocklin, K.A.Wheeler, J.Budworth, A.L.Dodds, M.J.Pallen, D.J.Maskell, I.G.Charles, and A.R.Hawkins (2002).
PDZ domains facilitate binding of high temperature requirement protease A (HtrA) and tail-specific protease (Tsp) to heterologous substrates through recognition of the small stable RNA A (ssrA)-encoded peptide.
  J Biol Chem, 277, 39443-39449.  
11741967 A.Y.Hung, and M.Sheng (2002).
PDZ domains: structural modules for protein complex assembly.
  J Biol Chem, 277, 5699-5702.  
12119305 D.L.Silver (2002).
A carboxyl-terminal PDZ-interacting domain of scavenger receptor B, type I is essential for cell surface expression in liver.
  J Biol Chem, 277, 34042-34047.  
12437101 H.Brandstetter, J.S.Kim, M.Groll, P.Göttig, and R.Huber (2002).
Structural basis for the processive protein degradation by tricorn protease.
  Biol Chem, 383, 1157-1165.  
11741964 M.Paetzel, R.E.Dalbey, and N.C.Strynadka (2002).
Crystal structure of a bacterial signal peptidase apoenzyme: implications for signal peptide binding and the Ser-Lys dyad mechanism.
  J Biol Chem, 277, 9512-9519.
PDB code: 1kn9
12032552 M.R.Maurizi (2002).
Love it or cleave it: tough choices in protein quality control.
  Nat Struct Biol, 9, 410-412.  
12032064 S.Shin, T.H.Lee, N.C.Ha, H.M.Koo, S.Y.Kim, H.S.Lee, Y.S.Kim, and B.H.Oh (2002).
Structure of malonamidase E2 reveals a novel Ser-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature.
  EMBO J, 21, 2509-2516.
PDB codes: 1ock 1ocl 1ocm
11967569 W.Li, S.M.Srinivasula, J.Chai, P.Li, J.W.Wu, Z.Zhang, E.S.Alnemri, and Y.Shi (2002).
Structural insights into the pro-apoptotic function of mitochondrial serine protease HtrA2/Omi.
  Nat Struct Biol, 9, 436-441.
PDB code: 1lcy
11115631 B.A.Diner (2001).
Amino acid residues involved in the coordination and assembly of the manganese cluster of photosystem II. Proton-coupled electron transport of the redox-active tyrosines and its relationship to water oxidation.
  Biochim Biophys Acta, 1503, 147-163.  
11687660 E.Zak, B.Norling, R.Maitra, F.Huang, B.Andersson, and H.B.Pakrasi (2001).
The initial steps of biogenesis of cyanobacterial photosystems occur in plasma membranes.
  Proc Natl Acad Sci U S A, 98, 13443-13448.  
11312137 M.Estelle (2001).
Proteases and cellular regulation in plants.
  Curr Opin Plant Biol, 4, 254-260.  
11825690 M.J.Pallen, A.C.Lam, and N.Loman (2001).
Tricorn-like proteases in bacteria.
  Trends Microbiol, 9, 518-521.  
11551506 Y.Luo, R.A.Pfuetzner, S.Mosimann, M.Paetzel, E.A.Frey, M.Cherney, B.Kim, J.W.Little, and N.C.Strynadka (2001).
Crystal structure of LexA: a conformational switch for regulation of self-cleavage.
  Cell, 106, 585-594.
PDB codes: 1jhc 1jhe 1jhf 1jhh
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.