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PDBsum entry 1rmg

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Hydrolase PDB id
1rmg
Jmol
Contents
Protein chain
422 a.a. *
Ligands
NAG-NAG-BMA-MAN-
BMA
NAG-NAG-BMA
MAN ×14
BMA ×3
GLC
Waters ×177
* Residue conservation analysis
PDB id:
1rmg
Name: Hydrolase
Title: Rhamnogalacturonase a from aspergillus aculeatus
Structure: Rhamnogalacturonase a. Chain: a. Synonym: rgase a. Engineered: yes
Source: Aspergillus aculeatus. Organism_taxid: 5053. Expressed in: aspergillus oryzae. Expression_system_taxid: 5062
Resolution:
2.00Å     R-factor:   0.174     R-free:   0.214
Authors: T.N.Petersen,S.Kauppinen,S.Larsen
Key ref:
T.N.Petersen et al. (1997). The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix. Structure, 5, 533-544. PubMed id: 9115442 DOI: 10.1016/S0969-2126(97)00209-8
Date:
26-Feb-97     Release date:   04-Mar-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q00001  (RHGA_ASPAC) -  Rhamnogalacturonase A
Seq:
Struc:
440 a.a.
422 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.171  - Rhamnogalacturonan hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
DOI no: 10.1016/S0969-2126(97)00209-8 Structure 5:533-544 (1997)
PubMed id: 9115442  
 
 
The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix.
T.N.Petersen, S.Kauppinen, S.Larsen.
 
  ABSTRACT  
 
BACKGROUND: Pectic substances are the major polysaccharide components of the middle lamella and primary cell wall of dicotyledonous plants. They consist of homogalacturonan 'smooth' regions and highly rhamnified 'hairy' regions of rhamnogalacturonan. The backbone in rhamnogalacturonan-l (RG-l), which is composed of alternating galacturonic acid and rhamnose residues, is the substrate for a new class of enzymes known as rhamnogalacturnoases (RGases). RGase A is a novel enzyme implicated in the enzymatic degradation of RG-l. RESULTS: The structure of RGase A from Aspergillus aculeatus has been solved by the single isomorphous replacement method including anomalous scattering (SIRAS method) to 2.0 A resolution. The enzyme folds into a large right-handed parallel beta helix, with a core composed of 13 turns of beta strands. Four parallel beta sheets (PB1, PB1a, PB2 and PB3), formed by the consecutive turns, are typically separated by a residue in the conformation of a left-handed alpha helix. As a consequence of the consecutive turns, 32% of all residues have their sidechains aligned at the surface or in the interior of the parallel beta helix. The aligned residues at the surface are dominated by threonine, aspartic acid and asparagine, whereas valine, leucine and isoleucine are most frequently found in the interior. A very large hydrophobic cavity is found in the interior of the parallel beta helix. The potential active site is a groove, oriented almost perpendicular to the helical axis, containing a cluster of three aspartic acid residues and one glutamic acid residue. The enzyme is highly glycosylated; two N-linked and eighteen O-linked glycosylation sites have been found in the structure. CONCLUSIONS: Rhamnogalacturonase A from A. aculeatus is the first three-dimensional structure of an enzyme hydrolyzing glycoside bonds within the backbone of RG-l. The large groove, which is the potential active site of RGase A, is also seen in the structures of pectate lyases. Two catalytic aspartic acid residues, which have been proposed to have a catalytic role, reside in this area of RGase A. The distance between the aspartic acid residues is consistent with the inverting mechanism of catalysis. The glycan groups bound to RGase A are important to the stability of the crystal, as the carbohydrate moiety is involved in most of the intermolecular hydrogen bonds.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. A stereo view of the Ca trace of RGase A. The enzyme folds into a coiled parallel b-helix structure.
 
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 533-544) copyright 1997.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
17823855 D.Wong (2008).
Enzymatic deconstruction of backbone structures of the ramified regions in pectins.
  Protein J, 27, 30-42.  
17957779 I.Martínez-Martínez, J.Navarro-Fernández, J.Daniel Lozada-Ramírez, F.García-Carmona, and A.Sánchez-Ferrer (2008).
YesT: a new rhamnogalacturonan acetyl esterase from Bacillus subtilis.
  Proteins, 71, 379-388.  
18083818 J.Navarro-Fernández, I.Martínez-Martínez, S.Montoro-García, F.García-Carmona, H.Takami, and A.Sánchez-Ferrer (2008).
Characterization of a new rhamnogalacturonan acetyl esterase from Bacillus halodurans C-125 with a new putative carbohydrate binding domain.
  J Bacteriol, 190, 1375-1382.  
17220218 J.C.Fong, and F.H.Yildiz (2007).
The rbmBCDEF gene cluster modulates development of rugose colony morphology and biofilm formation in Vibrio cholerae.
  J Bacteriol, 189, 2319-2330.  
16550377 G.Michel, P.Nyval-Collen, T.Barbeyron, M.Czjzek, and W.Helbert (2006).
Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases.
  Appl Microbiol Biotechnol, 71, 23-33.  
16522010 R.Stern, and M.J.Jedrzejas (2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
  Chem Rev, 106, 818-839.  
17053784 Y.Xiang, M.C.Morais, A.J.Battisti, S.Grimes, P.J.Jardine, D.L.Anderson, and M.G.Rossmann (2006).
Structural changes of bacteriophage phi29 upon DNA packaging and release.
  EMBO J, 25, 5229-5239.  
16262687 L.D.Kluskens, G.J.van Alebeek, J.Walther, A.G.Voragen, W.M.de Vos, and J.van der Oost (2005).
Characterization and mode of action of an exopolygalacturonase from the hyperthermophilic bacterium Thermotoga maritima.
  FEBS J, 272, 5464-5473.  
15968068 S.A.Douthit, M.Dlakic, D.E.Ohman, and M.J.Franklin (2005).
Epimerase active domain of Pseudomonas aeruginosa AlgG, a protein that contains a right-handed beta-helix.
  J Bacteriol, 187, 4573-4583.  
15155751 G.Michel, K.Pojasek, Y.Li, T.Sulea, R.J.Linhardt, R.Raman, V.Prabhakar, R.Sasisekharan, and M.Cygler (2004).
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
  J Biol Chem, 279, 32882-32896.
PDB codes: 1ofl 1ofm
15560783 H.Akeboshi, T.Tonozuka, T.Furukawa, K.Ichikawa, H.Aoki, A.Shimonishi, A.Nishikawa, and Y.Sakano (2004).
Insights into the reaction mechanism of glycosyl hydrolase family 49. Site-directed mutagenesis and substrate preference of isopullulanase.
  Eur J Biochem, 271, 4420-4427.  
14670977 J.Jenkins, V.E.Shevchik, N.Hugouvieux-Cotte-Pattat, and R.W.Pickersgill (2004).
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.
  J Biol Chem, 279, 9139-9145.
PDB code: 1ru4
14997537 J.K.Choi, B.H.Lee, C.H.Chae, and W.Shin (2004).
Computer modeling of the rhamnogalacturonase-"hairy" pectin complex.
  Proteins, 55, 22-33.  
12962629 A.M.Larsson, R.Andersson, J.Ståhlberg, L.Kenne, and T.A.Jones (2003).
Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex.
  Structure, 11, 1111-1121.
PDB codes: 1ogm 1ogo
11910025 J.F.Kreisberg, S.D.Betts, C.Haase-Pettingell, and J.King (2002).
The interdigitated beta-helix domain of the P22 tailspike protein acts as a molecular clamp in trimer stabilization.
  Protein Sci, 11, 820-830.  
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.  
12136151 R.Kadirvelraj, P.Harris, J.C.Poulsen, S.Kauppinen, and S.Larsen (2002).
A stepwise optimization of crystals of rhamnogalacturonan lyase from Aspergillus aculeatus.
  Acta Crystallogr D Biol Crystallogr, 58, 1346-1349.  
12022868 T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, and H.Kato (2002).
Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
  Biochemistry, 41, 6651-6659.
PDB codes: 1k5c 1kcc 1kcd
11544130 F.Micheli (2001).
Pectin methylesterases: cell wall enzymes with important roles in plant physiology.
  Trends Plant Sci, 6, 414-419.  
  11493601 G.Michel, L.Chantalat, E.Fanchon, B.Henrissat, B.Kloareg, and O.Dideberg (2001).
The iota-carrageenase of Alteromonas fortis. A beta-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide.
  J Biol Chem, 276, 40202-40209.
PDB code: 1h80
11687632 L.Federici, C.Caprari, B.Mattei, C.Savino, A.Di Matteo, G.De Lorenzo, F.Cervone, and D.Tsernoglou (2001).
Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein).
  Proc Natl Acad Sci U S A, 98, 13425-13430.
PDB code: 1hg8
11717490 M.Akita, A.Suzuki, T.Kobayashi, S.Ito, and T.Yamane (2001).
The first structure of pectate lyase belonging to polysaccharide lyase family 3.
  Acta Crystallogr D Biol Crystallogr, 57, 1786-1792.
PDB code: 1ee6
11729262 R.P.de Vries, and J.Visser (2001).
Aspergillus enzymes involved in degradation of plant cell wall polysaccharides.
  Microbiol Mol Biol Rev, 65, 497.  
11468409 T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, and H.Kato (2001).
Crystallization and preliminary X-ray study of endopolygalacturonase from the pathogenic fungus Stereum purpureum.
  Acta Crystallogr D Biol Crystallogr, 57, 1171-1173.  
10801485 A.Mølgaard, S.Kauppinen, and S.Larsen (2000).
Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases.
  Structure, 8, 373-383.
PDB codes: 1deo 1dex
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
11112543 J.A.Benen, H.C.Kester, L.Parenicová, and J.Visser (2000).
Characterization of Aspergillus niger pectate lyase A.
  Biochemistry, 39, 15563-15569.  
10653812 R.Khurana, and A.L.Fink (2000).
Do parallel beta-helix proteins have a unique fourier transform infrared spectrum?
  Biophys J, 78, 994.  
10617668 S.Armand, M.J.Wagemaker, P.Sánchez-Torres, H.C.Kester, Y.van Santen, B.W.Dijkstra, J.Visser, and J.A.Benen (2000).
The active site topology of Aspergillus niger endopolygalacturonase II as studied by site-directed mutagenesis.
  J Biol Chem, 275, 691-696.  
10922032 S.R.Herron, J.A.Benen, R.D.Scavetta, J.Visser, and F.Jurnak (2000).
Structure and function of pectic enzymes: virulence factors of plant pathogens.
  Proc Natl Acad Sci U S A, 97, 8762-8769.  
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.  
10089438 R.Pickersgill, M.Scott, D.Smith, K.Worboys, and J.Jenkins (1999).
Crystallization and preliminary crystallographic analysis of the endo-polygalacturonase from Erwinia carotovora ssp. carotovora.
  Acta Crystallogr D Biol Crystallogr, 55, 320-322.  
10521427 Y.van Santen, J.A.Benen, K.H.Schröter, K.H.Kalk, S.Armand, J.Visser, and B.W.Dijkstra (1999).
1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis.
  J Biol Chem, 274, 30474-30480.
PDB code: 1czf
  9655353 A.Bateman, A.G.Murzin, and S.A.Teichmann (1998).
Structure and distribution of pentapeptide repeats in bacteria.
  Protein Sci, 7, 1477-1480.  
9733763 R.Pickersgill, D.Smith, K.Worboys, and J.Jenkins (1998).
Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora.
  J Biol Chem, 273, 24660-24664.
PDB code: 1bhe
9636063 S.Miller, B.Schuler, and R.Seckler (1998).
A reversibly unfolding fragment of P22 tailspike protein with native structure: the isolated beta-helix domain.
  Biochemistry, 37, 9160-9168.  
9345621 B.Henrissat, and G.Davies (1997).
Structural and sequence-based classification of glycoside hydrolases.
  Curr Opin Struct Biol, 7, 637-644.  
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.