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17  structures 257  species 3  interactions 293  sequences 7  architectures

Family: Glyco_hydro_67C (PF07477)

Summary: Glycosyl hydrolase family 67 C-terminus

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This is the Wikipedia entry entitled "Glycoside hydrolase family 67". More...

Glycoside hydrolase family 67 Edit Wikipedia article

Glycosyl hydrolase family 67 N-terminus
PDB 1k9d EBI.jpg
the 1.7 a crystal structure of alpha-d-glucuronidase, a family-67 glycoside hydrolase from bacillus stearothermophilus t-1
Identifiers
Symbol Glyco_hydro_67N
Pfam PF03648
InterPro IPR005154
SCOP 1h41
SUPERFAMILY 1h41
CAZy GH67
Glycosyl hydrolase family 67 middle domain
PDB 1h41 EBI.jpg
pseudomonas cellulosa e292a alpha-d-glucuronidase mutant complexed with aldotriuronic acid
Identifiers
Symbol Glyco_hydro_67M
Pfam PF07488
InterPro IPR011100
SCOP 1h41
SUPERFAMILY 1h41
CAZy GH67
Glycosyl hydrolase family 67 C-terminus
PDB 1k9d EBI.jpg
the 1.7 a crystal structure of alpha-d-glucuronidase, a family-67 glycoside hydrolase from bacillus stearothermophilus t-1
Identifiers
Symbol Glyco_hydro_67C
Pfam PF07477
InterPro IPR011099
SCOP 1h41
SUPERFAMILY 1h41
CAZy GH67

In molecular biology, glycoside hydrolase family 67 is a family of glycoside hydrolases.

Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families.[1][2][3] This classification is available on the CAZy(http://www.cazy.org/GH1.html) web site,[4] and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.[5]

Glycoside hydrolase family 67 includes alpha-glucuronidases, these are components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans.

Members of this family consist of three structural domains. Deletion mutants of alpha-glucuronidase from Bacillus stearothermophilus have indicated that the central region is responsible for the catalytic activity. Within this central domain, the invariant Glu and Asp (residues 391 and 364 respectively from Bacillus stearothermophilus) are thought to from the catalytic centre.[6] The C-terminal region of alpha-glucuronidase is mainly alpha-helical. It wraps around the catalytic domain, making additional interactions both with the N-terminal domain of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer.[7]

References[edit]

  1. ^ Henrissat B, Callebaut I, Mornon JP, Fabrega S, Lehn P, Davies G (1995). "Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases". Proc. Natl. Acad. Sci. U.S.A. 92 (15): 7090–7094. doi:10.1073/pnas.92.15.7090. PMC 41477. PMID 7624375. 
  2. ^ Henrissat B, Davies G (1995). "Structures and mechanisms of glycosyl hydrolases". Structure 3 (9): 853–859. doi:10.1016/S0969-2126(01)00220-9. PMID 8535779. 
  3. ^ Bairoch, A. "Classification of glycosyl hydrolase families and index of glycosyl hydrolase entries in SWISS-PROT". 1999.
  4. ^ Henrissat, B. and Coutinho P.M. "Carbohydrate-Active Enzymes server". 1999.
  5. ^ CAZypedia, an online encyclopedia of carbohydrate-active enzymes.
  6. ^ Shoham Y, Zaide G, Shallom D, Shulami S, Zolotnitsky G, Golan G, Baasov T, Shoham G (2001). "Biochemical characterization and identification of catalytic residues in alpha-glucuronidase from Bacillus stearothermophilus T-6". Eur. J. Biochem. 268 (10): 3006–3016. doi:10.1046/j.1432-1327.2001.02193.x. PMID 11358519. 
  7. ^ Nurizzo D, Nagy T, Gilbert HJ, Davies GJ (April 2002). "The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A". Structure 10 (4): 547–56. PMID 11937059. 

This article incorporates text from the public domain Pfam and InterPro IPR011099

This article incorporates text from the public domain Pfam and InterPro IPR011100

This article incorporates text from the public domain Pfam and InterPro IPR005154

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Glycosyl hydrolase family 67 C-terminus Provide feedback

Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the C terminal region of alpha-glucuronidase which is mainly alpha-helical. It wraps around the catalytic domain (PF07488), making additional interactions both with the N-terminal domain (PF03648) of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer [1].

Literature references

  1. Nurizzo D, Nagy T, Gilbert HJ, Davies GJ; , Structure (Camb) 2002;10:547-556.: The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. PUBMED:11937059 EPMC:11937059


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011099

Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the C-terminal region of alpha-glucuronidase, which is mainly alpha-helical. It wraps around the catalytic domain (INTERPRO), making additional interactions both with the N-terminal domain (INTERPRO) of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer [PUBMED:11937059].

Gene Ontology

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Domain organisation

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(38)
Full
(293)
Representative proteomes NCBI
(306)
Meta
(20)
RP15
(42)
RP35
(84)
RP55
(108)
RP75
(125)
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  Seed
(38)
Full
(293)
Representative proteomes NCBI
(306)
Meta
(20)
RP15
(42)
RP35
(84)
RP55
(108)
RP75
(125)
Alignment:
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  Seed
(38)
Full
(293)
Representative proteomes NCBI
(306)
Meta
(20)
RP15
(42)
RP35
(84)
RP55
(108)
RP75
(125)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

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Seed source: CAZY
Previous IDs: none
Type: Domain
Author: Finn RD, Moxon SJ
Number in seed: 38
Number in full: 293
Average length of the domain: 220.20 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 31.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.8 28.8
Noise cut-off 19.3 19.9
Model length: 225
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

Glyco_hydro_67C Glyco_hydro_67N Glyco_hydro_67M

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Glyco_hydro_67C domain has been found. There are 17 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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