SMART: PbH1 domain annotation

PbH1 Parallel beta-helix repeats

SMART accession number:	SM00710
Description:	The tertiary structures of pectate lyases and rhamnogalacturonase A show a stack of parallel beta strands that are coiled into a large helix. Each coil of the helix represents a structural repeat that, in some homologues, can be recognised from sequence information alone. Conservation of asparagines might be connected with asparagine-ladders that contribute to the stability of the fold. Proteins containing these repeats most often are enzymes with polysaccharide substrates.
Interpro abstract (IPR006626):	The tertiary structures of pectate lyases and rhamnogalacturonase A show a stack of parallel beta strands that are coiled into a large helix. Each coil of the helix represents a structural repeat that, in some homologues, can be recognised from sequence information alone. Conservation of asparagines might be connected with asparagine-ladders that contribute to the stability of the fold. Proteins containing these repeats most often are enzymes with polysaccharide substrates [(PUBMED:9724625)].
Family alignment:	View or

There are 44080 PbH1 domains in 6613 proteins in SMART's nrdb database.

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Evolution (species in which this domain is found)
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This tree shows only several representative species. The complete taxonomic breakdown of all proteins with PbH1 domain is also avaliable.

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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes
Cellular role (predicted cellular role)
Binding / catalysis: Polysaccharide hydrolysis
Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Bedford MT, Leder P
- The FF domain: a novel motif that often accompanies WW domains.
- Trends Biochem Sci. 1999; 24: 264-5
- Jenkins J, Mayans O, Pickersgill R
- Structure and evolution of parallel beta-helix proteins.
- J Struct Biol. 1998; 122: 236-46
- Display abstract
- Three bacterial pectate lyases, a pectin lyase from Aspergillus niger, thestructures of rhamnogalacturonase A from Aspergillus aculeatus, RGase A,and the P22-phage tailspike protein, TSP, display the right-handedparallel beta-helix architecture first seen in pectate lyase. The lyaseshave 7 complete coils while RGase A and TSP have 11 and 12, respectively.Each coil contains three beta-strands and three turn regions named PB1,T1, PB2, T2, PB3, and T3 in their order of occurrence. The lyases havehomologous sequences but RGase A and TSP do not show obvious sequencehomology either to the lyases or to each other. However, the structuralsimilarities between all these molecules are so extensive that divergencefrom a common ancestor is much more probable than convergence to the samefold. The region PB2-T2-PB3 is the best conserved region in the lyases andshows the clearest structural similarity. Not only is the pleating and thedirection of the hydrogen bonding in the sheets conserved, but so is theunusual alphaL-conformation turn between the two sheets. However, theoverall shape, the position of long loops, a conserved alpha-helix thatcovers the amino-terminal end of the parallel beta-helix and stacks ofresidues in alphaR-conformation at the start of PB1 all suggest a commonancestor. The functional similarity, that the enzymes all bindalpha-galactose containing polymers at an equivalent site involving PB1and its two flanking turn regions, further supports divergent evolution.We suggest that the stacking of the coils and the unusual nearperpendicular junction of PB2 and PB3 make the parallel beta-helix foldespecially likely to maintain similar main chain conformations duringdivergent evolution even after all vestige of similarity in primarystructure has vanished.
- Pickersgill R, Smith D, Worboys K, Jenkins J
- Crystal structure of polygalacturonase from Erwinia carotovora ssp.carotovora.
- J Biol Chem. 1998; 273: 24660-4
- Display abstract
- The crystal structure of the 40-kDa endo-polygalacturonase from Erwiniacarotovora ssp. carotovora was solved by multiple isomorphous replacementand refined at 1.9 A to a conventional crystallographic R-factor of 0.198and Rfree of 0.239. This is the first structure of a polygalacturonase andcomprises a 10 turn right-handed parallel beta-helix domain with two loopregions forming a "tunnel like" substrate-binding cleft. Sequenceconservation indicates that the active site of polygalacturonase isbetween these two loop regions, and comparison of the structure ofpolygalacturonase with that of rhamnogalacturonase A from Aspergillusaculeatus enables two conserved aspartates, presumed to be catalyticresidues, to be identified. An adjacent histidine, in accord withbiochemical results, is also seen. A similarity in overall electrostaticproperties of the substrate-binding clefts of polygalacturonase andpectate lyase, which bind and cleave the same substrate, polygalacturonicacid, is also revealed.
- Rotin D
- WW (WWP) domains: from structure to function.
- Curr Top Microbiol Immunol. 1998; 228: 115-33
- Jurnak F, Yoder MD, Pickersgill R, Jenkins J
- Parallel beta-domains: a new fold in protein structures.
- Curr Opin Struct Biol. 1994; 4: 802-6
- Display abstract
- A new type of structural domain, composed of parallel beta-strands foldedinto a coiled structure, has been observed in several protein structureswithin the past year. An analysis of the basic motif indicates that thereare two distinct types, with variations likely to be discovered in thefuture.
- Yoder MD, Lietzke SE, Jurnak F
- Unusual structural features in the parallel beta-helix in pectate lyases.
- Structure. 1993; 1: 241-51
- Display abstract
- BACKGROUND: A new type of domain structure, an all parallel beta class,has recently been observed in two pectate lyases, PelC and PelE. Theatomic models have been analyzed to determine whether the new tertiaryfold exhibits unusual structural features. RESULTS: The polypeptidebackbone exhibits no new types of secondary structural elements. However,novel features occur in the amino acid side chain interactions. The sidechain atoms form linear stacks that include asparagine ladders, serinestacks, aliphatic stacks, and ringed-residue stacks. A new type ofbeta-sandwich between parallel beta-sheets is observed with propertiesthat are more characteristic of antiparallel beta-sheets. CONCLUSION: Ananalysis of the PelC and PelE structures, belonging to an all parallelbeta structural class, reveals novel amino acid side chain interactions, anew type of beta-sandwich and an atypical amino acid composition ofparallel beta-sheets. The findings are relevant to three-dimensionalstructural predictions.
- Yoder MD, Keen NT, Jurnak F
- New domain motif: the structure of pectate lyase C, a secreted plantvirulence factor.
- Science. 1993; 260: 1503-7
- Display abstract
- Pectate lyases are secreted by pathogens and initiate soft-rot diseases inplants by cleaving polygalacturonate, a major component of the plant cellwall. The three-dimensional structure of pectate lyase C from Erwiniachrysanthemi has been solved and refined to a resolution of 2.2 angstroms.The enzyme folds into a unique motif of parallel beta strands coiled intoa large helix. Within the core, the amino acids form linear stacks andinclude a novel asparagine ladder. The sequence similarities that pectatelyases share with pectin lyases, pollen and style proteins, and tubulinssuggest that the parallel beta helix motif may occur in a broad spectrumof proteins.
Metabolism (metabolic pathways involving proteins which contain this domain)

Structure (3D structures containing this domain)

3D Structures of PbH1 domains in PDB

PDB code	Main view	Title
1bhe		Polygalacturonase from erwinia carotovora ssp. carotovora
1clw		Tailspike protein from phage p22, v331a mutant
1czf		Endo-polygalacturonase ii from aspergillus niger
1hg8		Endopolygalacturonase from the phytopathogenic fungus fusarium moniliforme
1ia5		Polygalacturonase from aspergillus aculeatus
1ib4		Crystal structure of polygalacturonase from aspergillus aculeatus at ph4.5
1k5c		Endopolygalacturonase i from stereum purpureum at 0.96 a resolution
1kcc		Endopolygalacturonase i from stereum purpureum complexed with a galacturonate at 1.00 a resolution.
1kcd		Endopolygalacturonase i from stereum purpureum complexed with two galacturonate at 1.15 a resolution.
1nhc		Structural insights into the processivity of endopolygalacturonase i from aspergillus niger
1qa1		Tailspike protein, mutant v331g
1qa2		Tailspike protein, mutant a334v
1qa3		Tailspike protein, mutant a334i
1qq1		Tailspike protein, mutant e359g
1qrb		Plasticity and steric strain in a parallel beta-helix: rational mutations in p22 tailspike protein
1rmg		Rhamnogalacturonase a from aspergillus aculeatus
1ru4		Crystal structure of pectate lyase pel9a
1tsp		Crystal structure of p22 tailspike protein: interdigitated subunits in a thermostable trimer
1tyu		Structure of tailspike-protein
1tyv		Structure of tailspike-protein
1tyw		Structure of tailspike-protein
1tyx		Title of tailspike-protein
1vbl		Structure of the thermostable pectate lyase pl 47
2iq7		Crystal structure of the polygalacturonase from colletotrichum lupini and its implications for the interaction with polygalacturonase-inhibiting proteins
2pyg		Azotobacter vinelandii mannuronan c-5 epimerase alge4 a- module
2pyh		Azotobacter vinelandii mannuronan c-5 epimerase alge4 a- module complexed with mannuronan trisaccharide
2v5i		Structure of the receptor-binding protein of bacteriophage det7: a podoviral tailspike in a myovirus
2vfm		Low temperature structure of p22 tailspike protein fragment (109-666)
2vfn		Low temperature structure of p22 tailspike protein fragment (109-666), mutant v125a
2vfo		Low temperature structure of p22 tailspike protein fragment (109-666), mutant v125l
2vfp		Low temperature structure of p22 tailspike protein fragment (109-666), mutant v349l
3gq7		Crystal structure of the bacteriophage phi29 gene product n-terminal fragment
3gq8		Crystal structure of the bacteriophage phi29 gene product n-terminal fragment in complex with 2-(n- cyclohexylamino)ethane sulfonic acid (ches)
3gq9		Crystal structure of the bacteriophage phi29 gene product n-terminal fragment in an apo form
3gqa		Crystal structure of the bacteriophage phi29 gene product n-terminal fragment in complex with cobalt ions
3gqn		Crystal structure of the pre-mature bacteriophage phi29 gene product 12
3jur		The crystal structure of a hyperthermoactive exopolygalacturonase from thermotoga maritima

Links (links to other resources describing this domain)
INTERPRO IPR006626