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36  structures 265  species 1  interaction 378  sequences 25  architectures

Family: ChitinaseA_N (PF08329)

Summary: Chitinase A, N-terminal domain

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This is the Wikipedia entry entitled "Chitinase A N-terminal domain". More...

Chitinase A N-terminal domain Edit Wikipedia article

ChitinaseA_N
PDB 1edq EBI.jpg
crystal structure of chitinase a from s. marcescens at 1.55 angstroms
Identifiers
Symbol ChitinaseA_N
Pfam PF08329
Pfam clan CL0159
InterPro IPR013540
SCOP 1ctn
SUPERFAMILY 1ctn

In molecular biology, the chitinase A N-terminal domain is found at the N-terminus of a number of bacterial chitinases and similar viral proteins. It is organised into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin.[1][2] It is separated by a hinge region from the catalytic domain; this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution.[1]

References[edit]

  1. ^ a b Perrakis A, Tews I, Dauter Z, Oppenheim AB, Chet I, Wilson KS, Vorgias CE (December 1994). "Crystal structure of a bacterial chitinase at 2.3 A resolution". Structure 2 (12): 1169–80. PMID 7704527. 
  2. ^ Perrakis A, Ouzounis C, Wilson KS (1997). "Evolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications". Fold Des 2 (5): 291–4. PMID 9377712. 

This article incorporates text from the public domain Pfam and InterPro IPR013540

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.

Chitinase A, N-terminal domain Provide feedback

This domain is found in a number of bacterial chitinases and similar viral proteins. It is organised into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin [1,2]. It is separated by a hinge region from the catalytic domain (PF00704); this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution [1].

Literature references

  1. Perrakis A, Tews I, Dauter Z, Oppenheim AB, Chet I, Wilson KS, Vorgias CE; , Structure 1994;2:1169-1180.: Crystal structure of a bacterial chitinase at 2.3 A resolution. PUBMED:7704527 EPMC:7704527

  2. Perrakis A, Ouzounis C, Wilson KS; , Fold Des 1997;2:291-294.: Evolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications. PUBMED:9377712 EPMC:9377712


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013540

This domain is found in a number of bacterial chitinases and similar viral proteins. It is organised into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin [PUBMED:7704527, PUBMED:9377712]. It is separated by a hinge region from the catalytic domain (INTERPRO); this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution [PUBMED:7704527].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan E-set (CL0159), which has the following description:

This clan includes a diverse range of domains that have an Ig-like fold and appear to be distantly related to each other. The clan includes: PKD domains, cadherins and several families of bacterial Ig-like domains as well as viral tail fibre proteins. it also includes several Fibronectin type III domain-containing families.

The clan contains the following 63 members:

A2M_N Alpha_adaptinC2 Big_1 Big_2 Big_3 Big_3_2 Big_3_3 Big_3_4 Big_4 Big_5 BiPBP_C BsuPI Cadherin Cadherin-like Cadherin_2 Cadherin_pro CARDB CHB_HEX_C CHB_HEX_C_1 ChitinaseA_N CHU_C Coatamer_beta_C COP-gamma_platf CopC DUF1034 DUF11 DUF1973 DUF2271 DUF4165 DUF4625 DUF916 EpoR_lig-bind Filamin FixG_C FlgD_ig fn3 Fn3_assoc He_PIG HYR IFNGR1 IL6Ra-bind Integrin_alpha2 Interfer-bind Invasin_D3 MG1 Mo-co_dimer Neurexophilin NPCBM_assoc PapD_N PKD PPC Qn_am_d_aIII REJ Rib SoxZ SprB SWM_repeat T2SS-T3SS_pil_N TIG Tissue_fac Transglut_C TRAP_beta Y_Y_Y

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(43)
Full
(378)
Representative proteomes NCBI
(351)
Meta
(4)
RP15
(13)
RP35
(26)
RP55
(38)
RP75
(56)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(43)
Full
(378)
Representative proteomes NCBI
(351)
Meta
(4)
RP15
(13)
RP35
(26)
RP55
(38)
RP75
(56)
Alignment:
Format:
Order:
Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(43)
Full
(378)
Representative proteomes NCBI
(351)
Meta
(4)
RP15
(13)
RP35
(26)
RP55
(38)
RP75
(56)
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:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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.

Note: You can also download the data file for the tree.

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.

Curation View help on the curation process

Seed source: Pfam-B_1049 (release 18.0)
Previous IDs: none
Type: Domain
Author: Fenech M
Number in seed: 43
Number in full: 378
Average length of the domain: 122.60 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 18.18 %

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 21.2 21.2
Trusted cut-off 21.2 21.3
Noise cut-off 21.1 20.6
Model length: 133
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Glyco_hydro_18

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 ChitinaseA_N domain has been found. There are 36 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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