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16  structures 1578  species 0  interactions 2006  sequences 5  architectures

Family: KduI (PF04962)

Summary: KduI/IolB family

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This is the Wikipedia entry entitled "KduI/IolB isomerase family". More...

KduI/IolB isomerase family Edit Wikipedia article

KduI/IolB family
PDB 1ywk EBI.jpg
crystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol-isomerase from enterococcus faecalis
Identifiers
Symbol KduI
Pfam PF04962
Pfam clan CL0029
InterPro IPR021120

In molecular biology, the KduI/IolB isomerase family is a family of isomerase enzymes.

The family includes 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (5-keto 4-deoxyuronate isomerase) (KduI) and 5-deoxy-glucuronate isomerase (5DG isomerase) (IolB).

KduI is involved in pectin degradation by free-living soil bacteria that use pectin as a carbon source, breaking it down to 2-keto-3-deoxygluconate, which can ultimately be converted to pyruvate. KduI catalyses the fourth step in pectin degradation, namely the interconversion of 5-keto-4-deoxyuronate and 2,5-diketo-3-dexoygluconate.[1] KduI has a TIM-barrel fold.[2]

This family also includes several bacterial Myo-inositol catabolism proteins, such as IolB, which is encoded by the inositol operon (iolABCDEFGHIJ) in Bacillus subtilis. IolB is involved in myo-inositol catabolism. Glucose repression of the iol operon induced by inositol is exerted through catabolite repression mediated by CcpA and the iol induction system mediated by IolR.[3] Members of this family possess a Cupin like structure.

References

  1. ^ Condemine G, Robert-Baudouy J (September 1991). "Analysis of an Erwinia chrysanthemi gene cluster involved in pectin degradation". Mol. Microbiol. 5 (9): 2191–202. doi:10.1111/j.1365-2958.1991.tb02149.x. PMID 1766386. 
  2. ^ Crowther RL, Georgiadis MM (November 2005). "The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli". Proteins 61 (3): 680–4. doi:10.1002/prot.20598. PMID 16152643. 
  3. ^ Miwa Y, Fujita Y (October 2001). "Involvement of two distinct catabolite-responsive elements in catabolite repression of the Bacillus subtilis myo-inositol (iol) operon". J. Bacteriol. 183 (20): 5877–84. doi:10.1128/JB.183.20.5877-5884.2001. PMC 99665. PMID 11566986. 

This article incorporates text from the public domain Pfam and InterPro IPR021120

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.

KduI/IolB family Provide feedback

This family includes the 5-keto 4-deoxyuronate isomerase enzyme EC:5.3.1.17 that is involved in pectin degradation. This family aldo includes bacterial Myo-inositol catabolism (IolB) proteins. The Bacillus subtilis inositol operon (iolABCDEFGHIJ) is involved in myo-inositol catabolism. Glucose repression of the iol operon induced by inositol is exerted through catabolite repression mediated by CcpA and the iol induction system mediated by IolR [2]. The exact function of IolB is unknown. Members of this family possess a Cupin like structure.

Literature references

  1. Condemine G, Robert-Baudouy J; , Mol Microbiol 1991;5:2191-2202.: Analysis of an Erwinia chrysanthemi gene cluster involved in pectin degradation. PUBMED:1766386 EPMC:1766386

  2. Miwa Y, Fujita Y; , J Bacteriol 2001;183:5877-5884.: Involvement of two distinct catabolite-responsive elements in catabolite repression of the Bacillus subtilis myo-inositol (iol) operon. PUBMED:11566986 EPMC:11566986


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR021120

The KduI/IolB family of enzymes includes 5-keto 4-deoxyuronate isomerase (KduI) and 5-deoxy-glucuronate isomerase (IolB).

KduI is involved in pectin degradation by free-living soil bacteria that use pectin as a carbon source, breaking it down to 2-keto-3-deoxygluconate, which can ultimately be converted to pyruvate. KduI catalyses the fourth step in pectin degradation, namely the interconversion of 5-keto-4-deoxyuronate and 2,5-diketo-3-dexoygluconate [PUBMED:1766386]. KduI has a TIM-barrel fold [PUBMED:16152643].

IolB is one of several bacterial proteins encoded by the inositol operon (iolABCDEFGHIJ) in Bacillus subtilis that are involved in myo-inositol catabolism. The enzyme is responsible for isomerization of 5-deoxy-D-glucuronic acid by IolB to produce 2-deoxy-5-keto-D-gluconic acid [PUBMED:18310071]. IolBs possess a cupin-like structure.

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 Cupin (CL0029), which has the following description:

This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.

The clan contains the following 53 members:

2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 dTDP_sugar_isom DUF1255 DUF1479 DUF1498 DUF1637 DUF1971 DUF386 DUF4437 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC KduI MannoseP_isomer Ofd1_CTDD Oxygenase-NA PhyH Pirin Pirin_C PMI_typeI Pox_C4_C10 TauD Tet_JBP VIT VIT_2

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
(72)
Full
(2006)
Representative proteomes NCBI
(1311)
Meta
(510)
RP15
(122)
RP35
(254)
RP55
(318)
RP75
(396)
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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
(72)
Full
(2006)
Representative proteomes NCBI
(1311)
Meta
(510)
RP15
(122)
RP35
(254)
RP55
(318)
RP75
(396)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(72)
Full
(2006)
Representative proteomes NCBI
(1311)
Meta
(510)
RP15
(122)
RP35
(254)
RP55
(318)
RP75
(396)
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.

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: COG3717 & Pfam-B_11840 (release 10.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 72
Number in full: 2006
Average length of the domain: 252.20 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 91.15 %

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 20.1 20.1
Trusted cut-off 20.1 20.6
Noise cut-off 20.0 19.8
Model length: 262
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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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 KduI domain has been found. There are 16 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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