Family Search for PF16332 (DUF4962)

Running HMMer for PF16332

PF16332 hits 15 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

BT4652 heparan sulfate cleaving enzyme from Bacteroides thetaiotaomicron VPI-5482
BT4652, BT_4652 conserved hypothetical protein from Bacteroides thetaiotaomicron VPI-5482
Aligns to 31:503 / 872 (54.2%), covers 100.0% of PF16332, 772.6 bits

• mutant phenotype: # Specifically important in carbon source Heparin sodium salt from porcine intestinal mucosa. 66% identical to the heparan sulfate cleaving enzyme ALJ58962.1 (PMID:30850540)
• Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet- and host-derived glycans
  Sartorio, Proceedings of the National Academy of Sciences of the United States of America 2023
  • “...enable glycan utilization. For example, proteins belonging to the heparin utilization PUL 85, such as BT_4652, BT_4675, and BT_4662 were particularly enriched in OMVs produced by cells cultured in the presence of heparin but not in the presence of the other glycans. Similarly, proteins encoded in...”
• Utilization of glycosaminoglycans by the human gut microbiota: participating bacteria and their enzymatic machineries
  Rawat, Gut microbes 2022
  • “...machinery of B. thetaiotaomicron Upon the induction by heparin and HS, the PUL spanning from bt4652 to bt4675 ( Figure 4 ) was found to be upregulated in B. thetaiotaomicron VPI-5482. 67 Various proteins encoded in this PUL have been comprehensively studied. 99 One surface-localized PL,...”
• Hedgehog pathway modulation by glypican 3-conjugated heparan sulfate
  Liu, Journal of cell science 2022
  • “...Genes encoding heparinases I, II and III (bt4675, bt4652 and bt4657) (Cartmell et al., 2017), and chondroitinase (bt3350), were cloned from Bacteroides...”
• Host glycan utilization within the Bacteroidetes Sus-like paradigm
  Brown, Glycobiology 2021
  • “...The growth on either substrate upregulates PULHep , from BT4652 to BT4663, as well as the 2O-sulfatase BT1596 and the PL13 BT4675 (Figure 1) (Martens et al....”
• How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans
  Cartmell, Proceedings of the National Academy of Sciences of the United States of America 2017
  • “...tag De-O-Sulfatase BT1596 Polysaccharide lyase family 15 BT4652 Inner membrane transporter BT4653 ROK family protein BT4654 TAT protein BT4655 De-O-Sulfatase...”
  • “...cultured on Hep indicate that only PULHep, extending from bt4652 to bt4675, was up-regulated in response to this GAG (16). The locus encodes PLs, sulfatases, a...”

6ljaA / B3C5J6 Crystal structure of exohep from bacteroides intestinalis dsm 17393 complexed with disaccharide product (see paper)
Aligns to 8:481 / 841 (56.4%), covers 100.0% of PF16332, 738.8 bits

• Ligands: 2-deoxy-6-o-sulfo-2-(sulfoamino)-alpha-d-glucopyranose; 4-deoxy-2-o-sulfo-alpha-l-threo-hex-4-enopyranuronic acid; calcium ion (6ljaA)

3aflA / A9CEJ9 Crystal structure of exotype alginate lyase atu3025 h531a complexed with alginate trisaccharide (see paper)
Aligns to 34:454 / 766 (55.0%), covers 83.4% of PF16332, 139.6 bits

• Ligands: alpha-l-gulopyranuronic acid; 4-deoxy-alpha-l-erythro-hex-4-enopyranuronic acid (3aflA)

A9CEJ9 guluronate-specific alginate lyase (EC 4.2.2.11); mannuronate-specific alginate lyase (EC 4.2.2.3) from Agrobacterium tumefaciens (see paper)
AAL43841.1 exotype alginate lyase (Atu3025) (EC 4.2.2.-) (see protein)
Atu3025 oligo alginate lyase from Agrobacterium tumefaciens str. C58 (Cereon)
Aligns to 44:464 / 776 (54.3%), covers 83.4% of PF16332, 139.5 bits

• Alginate Degradation: Insights Obtained through Characterization of a Thermophilic Exolytic Alginate Lyase
  Arntzen, Applied and environmental microbiology 2021 (secret)
• Expression and Characterization of a Cold-Adapted Alginate Lyase with Exo/Endo-Type Activity from a Novel Marine Bacterium Alteromonas portus HB161718^T
  Huang, Marine drugs 2021
  • “...exo-type alginate lyases reported so farfor example, AlgL17 from Microbulbifer sp. ALW1 [ 41 ], Atu3025 from Agrobacterium tumefaciens [ 39 ], Alg17C from Saccharophagus degradans 240 [ 42 ], and AlyFRB from Falsirhodobacter sp. alg1 [ 43 ]. In recent years, exo-type alginate lyase has...”
  • “...A. Yamasaki M. Mikami B. Hashimoto W. Murata K. Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens J. Biol. Chem. 2010 285 24519 24528 10.1074/jbc.M110.125450 20507980 40. Kersters K. De Ley J. The occurrence of the EntnerDoudoroff pathway in bacteria Antonie Van Leeuwenhoek 1968...”
• Glycoside Hydrolase Genes Are Required for Virulence of Agrobacterium tumefaciens on Bryophyllum daigremontiana and Tomato
  Mathews, Applied and environmental microbiology 2019
  • “...Atu0944 Atu1523 Atu1617 Atu1709 bglA xynA Atu2575 Atu2596 Atu3025 Atu3093 arfA Atu3128 pglA Atu3285 Atu3312 Atu3553 Atu3564 Atu3419 Atu4485 melA Atu5072 Atu5082...”
• Biochemical characteristics and synergistic effect of two novel alginate lyases from Photobacterium sp. FC615
  Lu, Biotechnology for biofuels 2019
  • “...phylogenetic tree, AlyPB2 was clustered with PL15 family together with the elucidated exolytic alginate lyases Atu3025 (NP_357573.1) from Agrobacterium tumefaciens strain C58 [ 27 , 46 ], A1-IV (AB011415.1) from Sphingomonas sp. A1 [ 25 , 26 ], OalA (EAP93067.1) from Vibrio splendidus 12B01 [ 28...”
  • “...OalA (93.4%, query cover 100%), as well as 42.1% sequence identity (query cover 89%) with Atu3025 and 39.9% (query cover 89%) and 38.1% (query cover 92%) sequence identity with A1-IV and AlyFRB, respectively. Heterologous expression of AlyPB1 and AlyPB2 in E. coli Heterologous expression systems for...”
• The molecular basis of endolytic activity of a multidomain alginate lyase from Defluviitalea phaphyphila, a representative of a new lyase family, PL39
  Ji, The Journal of biological chemistry 2019 (secret)
• Diversity of Three-Dimensional Structures and Catalytic Mechanisms of Alginate Lyases
  Xu, Applied and environmental microbiology 2018
  • “...to red in the C-terminal region. (B) Structure of Atu3025 from the PL15 family. The C-terminal, central, and N-terminal domains are colored in orange, cyan, and...”
  • “...exolytic bacterial alginate lyases. Exotype alginate lyase Atu3025 (PDB code 3A0O) from Agrobacterium tumefaciens, the only solved structure in this family,...”
• AlgM4: A New Salt-Activated Alginate Lyase of the PL7 Family with Endolytic Activity
  Huang, Marine drugs 2018
  • “...A1-IV, produced by the bacterial strain Sphingomonas sp. A1 [ 22 ], and alginate lyase Atu3025, produced by Agrobacterium tumefaciens C58 [ 23 ], possess exolytic activity and hydrolyze SA into mannuronate or guluronate. Alginate lyases that degrade alginate into monosaccharides are part of the PL15...”
  • “...A. Yamasaki M. Mikami B. Hashimoto W. Murata K. Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens J. Biol. Chem. 2010 285 24519 24528 10.1074/jbc.M110.125450 20507980 24. Garron M.L. Cygler M. Structural and mechanistic classification of uronic acid-containing polysaccharide lyases Glycobiology 2010 20 1547...”
• A Novel Bifunctional Endolytic Alginate Lyase with Variable Alginate-Degrading Modes and Versatile Monosaccharide-Producing Properties
  Peng, Frontiers in microbiology 2018
  • “...been identified, such as A1-IV from Sphingomonas sp. A1 ( Miyake et al., 2003 ), Atu3025 from Agrobacterium tumefaciens ( Ochiai et al., 2010 ), Alg17C from Saccharophagus degradans 2-40 ( Kim et al., 2012 ), and AlyA5 from Zobellia galactanivorans ( Thomas et al., 2013...”
  • “...Mikami B. Hashimoto W. Murata K. ( 2010 ). Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens . J. Biol. Chem. 285 24519 24528 . 10.1074/jbc.M110.125450 20507980 Papi M. Maiorana A. Bugli F. Torelli R. Posteraro B. Maulucci G. ( 2012 ). Detection of...”
• More

oal / Q9KWT4 oligoalginate lyase (EC 4.2.2.26) from Sphingomonas sp. (see 2 papers)
BAB03319.1 oligo alginate lyase (A1-IV;Oal) (EC 4.2.2.-) (see protein)
oal / BAB03319.1 oligo alginate lyase from Sphingomonas sp (see paper)
Aligns to 33:456 / 761 (55.7%), covers 84.7% of PF16332, 119.7 bits

Q5DWP2 mannuronate-specific alginate lyase (EC 4.2.2.3) from Sphingomonas sp. (see paper)
BAD90006.1 alginate lyase (A1-IV') (EC 4.2.2.3) (see protein)
Aligns to 37:404 / 812 (45.3%), covers 72.7% of PF16332, 85.0 bits

8khwA / A0A4V1YUP8 The crystal structure of glycosaminoglycan lyase gagase vii
Aligns to 24:290 / 582 (45.9%), covers 41.4% of PF16332, 36.5 bits

• Ligand: manganese (ii) ion (8khwA)

6jp4A / A0A4Y5UXE1 Crystal structure of the catalytic domain of a multi-domain alginate lyase dp0100 from thermophilic bacterium defluviitalea phaphyphila (see paper)
Aligns to 14:274 / 770 (33.9%), covers 36.1% of PF16332, 33.8 bits

• Ligands: manganese (ii) ion; magnesium ion; calcium ion (6jp4A)

E5X103 heparin lyase (EC 4.2.2.7) from Bacteroides eggerthii (see paper)
Aligns to 22:276 / 773 (33.0%), covers 34.9% of PF16332, 32.8 bits

C0JBW5 heparin lyase (EC 4.2.2.7) from Bacteroides stercoris (see paper)
ACN29695.1 acharan sulfate lyase 1/2 / heparin lyase II / heparanase II (AlsI;Als2;HepII) (EC 4.2.2.7|4.2.2.8|4.2.2.-) (see protein)
Aligns to 41:275 / 773 (30.4%), covers 34.9% of PF16332, 32.1 bits

3e80C / C6XZB6 Structure of heparinase ii complexed with heparan sulfate degradation disaccharide product (see paper)
Aligns to 16:290 / 747 (36.8%), covers 32.4% of PF16332, 30.4 bits

• Ligands: alpha-l-rhamnopyranose; 4-deoxy-alpha-l-threo-hex-4-enopyranuronic acid; zinc ion (3e80C)

hepB / C6XZB6 heparinase II (EC 4.2.2.8; EC 4.2.2.7) from Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3) (see 3 papers)
HEPB_PEDHD / C6XZB6 Heparin and heparin-sulfate lyase; Heparin lyase; Heparin-sulfate lyase; Heparinase II; HepII; EC 4.2.2.7; EC 4.2.2.8 from Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3) (see 3 papers)
ACU04612.1 heparin lyase II / heparinase II (HepB;Phep_2408) (EC 4.2.2.7|4.2.2.8) (see protein)
Aligns to 40:314 / 772 (35.6%), covers 32.4% of PF16332, 30.3 bits

• function: Cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Cleaves heparin at alpha-D- GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D- GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp.
  catalytic activity: Elimination of sulfate, appears to act on linkages between N- acetyl-D-glucosamine and uronate. Product is an unsaturated sugar.
  catalytic activity: Eliminative cleavage of polysaccharides containing (1->4)- linked D-glucuronate or L-iduronate residues and (1->4)-alpha-linked 2-sulfoamino-2-deoxy-6-sulfo-D-glucose residues to give oligosaccharides with terminal 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
  subunit: Homodimer.

6hznA / Q9UL01 Crystal structure of human dermatan sulfate epimerase 1
Aligns to 96:330 / 743 (31.6%), covers 33.6% of PF16332, 29.6 bits

• Ligand: manganese (ii) ion (6hznA)

DSE_BOVIN / P0C2H4 Dermatan-sulfate epimerase; DS epimerase; Chondroitin-glucuronate 5-epimerase; EC 5.1.3.19 from Bos taurus (Bovine) (see paper)
Aligns to 109:354 / 958 (25.7%), covers 33.8% of PF16332, 29.3 bits

• function: Converts D-glucuronic acid to L-iduronic acid (IdoUA) residues. Plays an important role in the biosynthesis of the glycosaminoglycan/mucopolysaccharide dermatan sulfate.
  catalytic activity: chondroitin 4'-sulfate = dermatan 4'-sulfate (RHEA:21084)
  cofactor: Mn(2+) (Also has weak activity in the presence of Mg(2+) or Ca(2+) ions.)

DSE / Q9UL01 dermatan-sulfate epimerase (EC 5.1.3.19) from Homo sapiens (see 4 papers)
DSE_HUMAN / Q9UL01 Dermatan-sulfate epimerase; DS epimerase; Chondroitin-glucuronate 5-epimerase; Squamous cell carcinoma antigen recognized by T-cells 2; SART-2; EC 5.1.3.19 from Homo sapiens (Human) (see 5 papers)
NP_001309866 dermatan-sulfate epimerase isoform a precursor from Homo sapiens
Aligns to 119:353 / 958 (24.5%), covers 33.6% of PF16332, 28.7 bits

• function: Converts D-glucuronic acid to L-iduronic acid (IdoUA) residues. Plays an important role in the biosynthesis of the glycosaminoglycan/mucopolysaccharide dermatan sulfate.
  catalytic activity: chondroitin 4'-sulfate = dermatan 4'-sulfate (RHEA:21084)
  cofactor: Mn(2+) (Also has weak activity in the presence of Mg(2+) or Ca(2+) ions.)
• Dermatan sulfate epimerase 1 expression and mislocalization may interfere with dermatan sulfate synthesis and breast cancer cell growth.
  Listik, Carbohydrate research 2020 (PubMed)
  • GeneRIF: Dermatan sulfate epimerase 1 expression and mislocalization may interfere with dermatan sulfate synthesis and breast cancer cell growth.
• DSE promotes aggressive glioma cell phenotypes by enhancing HB-EGF/ErbB signaling.
  Liao, PloS one 2018
  • GeneRIF: Study showed that DSE is frequently upregulated in human glioma tissue and cell lines and associated with a worse tumor grade and poor overall survival. Its knockdown suppresses malignant phenotypes, whereas DSE overexpression enhances glioma cell malignancy, both in vitro and in vivo. Mechanically, DSE modulates HB-EGF-induced EGFR/ErbB2 activity and downstream signaling.
• Dermatan sulfate epimerase 1 and dermatan 4-O-sulfotransferase 1 form complexes that generate long epimerized 4-O-sulfated blocks.
  Tykesson, The Journal of biological chemistry 2018
  • GeneRIF: DS-epi1, DS-epi2, and D4ST1 form homomers and are all part of a hetero-oligomeric complex where D4ST1 directly interacts with DS-epi1, but not with DS-epi2. The cooperation of DS-epi1 with D4ST1 may therefore explain the processive mode of the formation of iduronic acid blocks.
• Loss of dermatan sulfate epimerase (DSE) function results in musculocontractural Ehlers-Danlos syndrome.
  Müller, Human molecular genetics 2013 (PubMed)
  • GeneRIF: study identified a homozygous DSE missense mutation (c.803C>T, p.S268L) in a male child with musculocontractural type of Ehlers-Danlos syndrome; data indicate mutation affects the epimerase activity, resulting in reduced dermatan sulfate (DS) biosynthesis and an increased synthesis or an accumulation or reduced conversion of chondroitin sulfate
• Dermatan sulfate is involved in the tumorigenic properties of esophagus squamous cell carcinoma.
  Thelin, Cancer research 2012
  • GeneRIF: Dermatan sulfate epimerase 1 was highly upregulated in esophagus squamous cell carcinoma
• Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function.
  Pacheco, The Journal of biological chemistry 2009 (PubMed)
  • GeneRIF: Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function.
• Glypican-4 regulated actin cytoskeletal reorganization in glucocorticoid treated trabecular meshwork cells and involvement of Wnt/PCP signaling.
  Maddala, Journal of cellular physiology 2023
  • “...1.593 0.042 P06858 Lipoprotein lipase 2 1.502 0.042 Q14517 Protocadherin Fat 1 14 1.501 0.043 Q9UL01 Dermatan-sulfate epimerase 5 1.848 0.043 O94875 Sorbin and SH3 domain-containing protein 2 20 1.692 0.054 Abbreviation: TM, trabecular meshwork. TABLE 2 Proteins decreased in the cytoskeletome fraction of human TM...”
• Prediction of potential drug targets based on simple sequence properties.
  Li, BMC bioinformatics 2007
  • “...Q5HYA8 Meckelin 2.037 9 Q9NYG2 Palmitoyltransferase ZDHHC3 2.020 10 Q96MH6 Transmembrane protein 68 1.999 11 Q9UL01 Dermatan-sulfate epimerase 1.974 12 Q5SY80 Uncharacterized protein C1orf101 1.914 13 Q9BQ90 Kelch domain-containing protein 3 1.827 14 P20618 Proteasome subunit beta type 1 1.818 15 Q8IZU2 WD repeat protein 17...”

Or search for genetic data about PF16332 in the Fitness Browser