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PDBsum entry 2pec
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Lyase (acting on polysaccharides) PDB id
2pec

 

 

 

 

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Contents
Protein chain
352 a.a. *
Waters ×114
* Residue conservation analysis
PDB id:
2pec
Name: Lyase (acting on polysaccharides)
Title: The refined three-dimensional structure of pectate lyasE C from erwinia chrysanthemi at 2.2 angstroms resolution: implications for an enzymatic mechanism
Structure: Pectate lyasE C. Chain: a. Engineered: yes
Source: Erwinia chrysanthemi. Organism_taxid: 556. Gene: ppel410 of pelc
Resolution:
2.20Å     R-factor:   0.180    
Authors: M.D.Yoder,F.Jurnak
Key ref: M.D.Yoder and F.Jurnak (1995). Protein motifs. 3. The parallel beta helix and other coiled folds. Faseb J, 9, 335-342. PubMed id: 7896002
Date:
08-Aug-94     Release date:   14-Feb-95    
Supersedes: 1pec
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11073  (PLYC_DICCH) -  Pectate lyase C from Dickeya chrysanthemi
Seq:
Struc: 		375 a.a.
352 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.2.2  - pectate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Pectin and Pectate Lyases
      Reaction: Eliminative cleavage of pectate to give oligosaccharides with 4-deoxy- alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.

 

 
Faseb J 9:335-342 (1995)
PubMed id: 7896002  
 
 
Protein motifs. 3. The parallel beta helix and other coiled folds.
M.D.Yoder, F.Jurnak.
 
  ABSTRACT  
 
A new type of structural domain, composed of all parallel beta strands, has been observed within the last year. An analysis of the basic types suggests that there are two distinct classes: the parallel beta helices, which belong to a tri beta-strand category, and the beta roll, which belongs to a di beta-strand category. The novel structural features of each class are described and the proteins belonging to each category are summarized. Proteins with the parallel beta helix fold include three pectate lyases and the tailspike protein from P22 phage. Proteins with the beta roll fold include two alkaline proteases. Although the parallel beta composition is emphasized, the same set of proteins share another common structural feature with several other proteins containing alpha helices: the polypeptide backbone is folded into a coiled structure in which each coil has the same 3-dimensional arrangement of a group of secondary structural elements. In addition to parallel beta domains, the other groups include the alpha/beta coiled fold, as represented by ribonuclease inhibitor, and the alpha/alpha coiled fold, as represented by lipovitellin and soluble lytic transglycoslyase. Novel features of the alpha/beta and alpha/alpha coiled folds are summarized.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22466878 K.V.Korotkov, M.Sandkvist, and W.G.Hol (2012).
The type II secretion system: biogenesis, molecular architecture and mechanism.
  Nat Rev Microbiol, 10, 336-351.  
21330133 E.C.Schulz, and R.Ficner (2011).
Knitting and snipping: chaperones in β-helix folding.
  Curr Opin Struct Biol, 21, 232-239.  
20596756 S.Basu, A.Roy, A.Ghosh, A.Bera, D.Chattopadhyay, and K.Chakrabarti (2011).
Arg²³⁵ is an essential catalytic residue of Bacillus pumilus DKS1 pectate lyase to degum ramie fibre.
  Biodegradation, 22, 153-161.  
19847915 M.Junker, and P.L.Clark (2010).
Slow formation of aggregation-resistant beta-sheet folding intermediates.
  Proteins, 78, 812-824.  
19491937 P.M.Tessier, and S.Lindquist (2009).
Unraveling infectious structures, strain variants and species barriers for the yeast prion [PSI+].
  Nat Struct Mol Biol, 16, 598-605.  
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
  19164928 R.B.Wickner, H.K.Edskes, F.Shewmaker, T.Nakayashiki, A.Engel, L.McCann, and D.Kryndushkin (2007).
Yeast prions: evolution of the prion concept.
  Prion, 1, 94.  
16452425 A.Wietzorrek, H.Schwarz, C.Herrmann, and V.Braun (2006).
The genome of the novel phage Rtp, with a rosette-like tail tip, is homologous to the genome of phage T1.
  J Bacteriol, 188, 1419-1436.  
16597248 Y.Liu, J.Carbonell, P.Weigele, and V.Gopalakrishnan (2006).
Protein fold recognition using segmentation conditional random fields (SCRFs).
  J Comput Biol, 13, 394-406.  
15264254 E.F.Pettersen, T.D.Goddard, C.C.Huang, G.S.Couch, D.M.Greenblatt, E.C.Meng, and T.E.Ferrin (2004).
UCSF Chimera--a visualization system for exploratory research and analysis.
  J Comput Chem, 25, 1605-1612.  
11852237 F.D.Ciccarelli, R.R.Copley, T.Doerks, R.B.Russell, and P.Bork (2002).
CASH--a beta-helix domain widespread among carbohydrate-binding proteins.
  Trends Biochem Sci, 27, 59-62.  
12015881 L.Cowen, P.Bradley, M.Menke, J.King, and B.Berger (2002).
Predicting the beta-helix fold from protein sequence data.
  J Comput Biol, 9, 261-276.  
11914504 M.A.McDonough, C.Ryttersgaard, M.E.Bjørnvad, L.Lo Leggio, M.Schülein, S.O.Schrøder Glad, and S.Larsen (2002).
Crystallization and preliminary X-ray characterization of a thermostable pectate lyase from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 58, 709-711.  
11504559 C.W.Ward, and T.P.Garrett (2001).
The relationship between the L1 and L2 domains of the insulin and epidermal growth factor receptors and leucine-rich repeat modules.
  BMC Bioinformatics, 2, 4.  
11567103 D.E.Kamen, and R.W.Woody (2001).
A partially folded intermediate conformation is induced in pectate lyase C by the addition of 8-anilino-1-naphthalenesulfonate (ANS).
  Protein Sci, 10, 2123-2130.  
10737931 B.Schuler, F.Fürst, F.Osterroth, S.Steinbacher, R.Huber, and R.Seckler (2000).
Plasticity and steric strain in a parallel beta-helix: rational mutations in the P22 tailspike protein.
  Proteins, 39, 89.
PDB codes: 1qq1 1qrb 1qrc
10713524 C.N.Doan, M.K.Caughron, J.C.Myers, N.W.Breakfield, R.L.Oliver, and M.D.Yoder (2000).
Purification, crystallization and x-ray analysis of crystals of pectate lyase A from Exwinia chrysanthemi.
  Acta Crystallogr D Biol Crystallogr, 56, 351-353.  
  11206055 J.F.Kreisberg, S.D.Betts, and J.King (2000).
Beta-helix core packing within the triple-stranded oligomerization domain of the P22 tailspike.
  Protein Sci, 9, 2338-2343.  
10899428 L.C.Serpell (2000).
Alzheimer's amyloid fibrils: structure and assembly.
  Biochim Biophys Acta, 1502, 16-30.  
10393307 L.Federici, B.Mattei, C.Caprari, C.Savino, F.Cervone, and D.Tsernoglou (1999).
Crystallization and preliminary X-ray diffraction study of the endo-polygalacturonase from Fusarium moniliforme.
  Acta Crystallogr D Biol Crystallogr, 55, 1359-1361.  
9492738 N.D.Lazo, and D.T.Downing (1998).
Amyloid fibrils may be assembled from beta-helical protofibrils.
  Biochemistry, 37, 1731-1735.  
17708899 L.M.Traub (1997).
Clathrin-associated adaptor proteins - putting it all together.
  Trends Cell Biol, 7, 43-46.  
8946845 B.Kobe (1996).
Leucines on a roll.
  Nat Struct Biol, 3, 977-980.  
  8665839 C.Kisker, H.Schindelin, B.E.Alber, J.G.Ferry, and D.C.Rees (1996).
A left-hand beta-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila.
  EMBO J, 15, 2323-2330.
PDB code: 1thj
8855221 S.Steinbacher, U.Baxa, S.Miller, A.Weintraub, R.Seckler, and R.Huber (1996).
Crystal structure of phage P22 tailspike protein complexed with Salmonella sp. O-antigen receptors.
  Proc Natl Acad Sci U S A, 93, 10584-10588.
PDB codes: 1tyu 1tyv 1tyw 1tyx
7568142 M.Sargiacomo, P.E.Scherer, Z.Tang, E.Kübler, K.S.Song, M.C.Sanders, and M.P.Lisanti (1995).
Oligomeric structure of caveolin: implications for caveolae membrane organization.
  Proc Natl Acad Sci U S A, 92, 9407-9411.  
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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