Protein Family Models

Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain. [1]. 8873595. Interaction of pyridine nucleotide substrates with Escherichia. coli dihydrodipicolinate reductase: thermodynamic and structural. analysis of binary complexes.. Reddy SG, Scapin G, Blanchard JS;. Biochemistry 1996;35:13294-13302.. [2]. 9398235. Three-dimensional structure of Escherichia coli. dihydrodipicolinate reductase in complex with NADH and the. inhibitor 2,6-pyridinedicarboxylate.. Scapin G, Reddy SG, Zheng R, Blanchard JS;. Biochemistry 1997;36:15081-15088.. [3]. 7893645. Three-dimensional structure of Escherichia coli. dihydrodipicolinate reductase.. Scapin G, Blanchard JS, Sacchettini JC;. Biochemistry 1995;34:3502-3512. (from Pfam)

Date:

2024-08-14

In a variety of organisms, including plants and several eubacteria, isoprenoids are synthesised by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway [2]. [1]. 1521767. Sequence and characterization of the gcpE gene of Escherichia. coli.. Baker J, Franklin DB, Parker J;. FEMS Microbiol Lett 1992;73:175-180.. [2]. 11274098. GcpE is involved in the 2-C-methyl-D-erythritol 4-phosphate. pathway of isoprenoid biosynthesis in Escherichia coli.. Altincicek B, Kollas AK, Sanderbrand S, Wiesner J, Hintz M, Beck. E, Jomaa H;. J Bacteriol 2001;183:2411-2416. (from Pfam)

Date:

2024-08-14

This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site [3]. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB. [1]. 11276424. The DNA-repair protein AlkB, EGL-9, and leprecan define new. families of 2-oxoglutarate- and iron-dependent dioxygenases.. Aravind L, Koonin EV;. Genome Biol 2001;2:RESEARCH0007.. [2]. 9211872. Cloning of the human prolyl 4-hydroxylase alpha subunit isoform. alpha(II) and characterization of the type II enzyme tetramer.. The alpha(I) and alpha(II) subunits do not form a mixed. alpha(I)alpha(II)beta2 tetramer.. Annunen P, Helaakoski T, Myllyharju J, Veijola J, Pihlajaniemi. T, Kivirikko KI;. J Biol Chem 1997;272:17342-17348.. [3]. 7753822. Cloning, baculovirus expression, and characterization of a. second mouse prolyl 4-hydroxylase alpha-subunit isoform:. formation of an alpha 2 beta 2 tetramer with the protein. disulfide-isomerase/beta subunit.. Helaakoski T, Annunen P, Vuori K, MacNeil IA, Pihlajaniemi T,. Kivirikko KI;. Proc Natl Acad Sci U S A 1995;92:4427-4431.. [4]. 7791906. Crystal structure of isopenicillin N synthase is the first from. a new structural family of enzymes.. Roach PL, Clifton IJ, Fulop V, Harlos K, Barton GJ, Hajdu J,. Andersson I,. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

The mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis is essential in many eubacteria, plants, and the malaria parasite. The LytB gene is involved in the trunk line of the MEP pathway. [1]. 8432714. Identification of the Escherichia coli lytB gene, which is. involved in penicillin tolerance and control of the stringent. response.. Gustafson CE, Kaul S, Ishiguro EE;. J Bacteriol 1993;175:1203-1205.. [2]. 11818558. Studies on the nonmevalonate terpene biosynthetic pathway:. metabolic role of IspH (LytB) protein.. Rohdich F, Hecht S, Gartner K, Adam P, Krieger C, Amslinger S,. Arigoni D, Bacher A, Eisenreich W. Proc Natl Acad Sci U S A 2002;99:1158-11563.. [3]. 11741609. Identification of (E)-4-hydroxy-3-methyl-but-2-enyl. pyrophosphate as a major activator for human gammadelta T cells. in Escherichia coli.. Hintz M, Reichenberg A, Altincicek B, Bahr U, Gschwind RM,. Kollas AK, Beck E, Wiesner J, Eberl M, Jomaa H. FEBS Lett 2001;509:317-322.. [4]. 11717301. The lytB gene of Escherichia coli is essential and specifies a. product needed for isoprenoid biosynthesis.. McAteer S, Coulson A, McLennan N, Masters M. J Bacteriol 2001;183:7403-7407.. [5]. 11418107. LytB, a novel gene of the 2-C-methyl-D-erythritol 4-phosphate. pathway of isoprenoid biosynthesis in Escherichia coli.. Altincicek B, Kollas A, Eberl M, Wiesner J, Sanderbrand S, Hintz. M, Beck E, Jomaa H. FEBS Lett 2001;499:37-40.. [6]. 11004185. Evidence of a role for LytB in the nonmevalonate pathway of. isoprenoid biosynthesis.. Cunningham FX Jr, Lafond TP, Gantt E. J Bacteriol 2000;182:5841-5848. (from Pfam)

Date:

2024-08-14

Members of this family include regulator of ribonuclease E activity A (RraA) and 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy- 4-hydroxy-2-oxoadipate (CHA) aldolase, also known as RraA-like protein [1]. RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing [2]. RraA-like proteins seem to contain aldolase and/or decarboxylase activity either in place of or in addition to the RNase E inhibitor functions [1]. [1]. 24359411. Biochemical and structural analysis of RraA proteins to decipher. their relationships with. 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipa. te aldolases.. Mazurkewich S, Wang W, Seah SY;. Biochemistry. 2014;53:542-553.. [2]. 14499605. The X-ray structure of Escherichia coli RraA (MenG), A protein. inhibitor of RNA processing.. Monzingo AF, Gao J, Qiu J, Georgiou G, Robertus JD;. J Mol Biol. 2003;332:1015-1024. (from Pfam)

Date:

2024-08-14

This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase. [1]. 9073078. The bphDEF meta-cleavage pathway genes involved in. biphenyl/polychlorinated biphenyl degradation are located on a. linear plasmid and separated from the initial bphACB genes in. Rhodococcus sp. strain RHA1.. Masai E, Sugiyama K, Iwashita N, Shimizu S, Hauschild JE, Hatta. T, Kimbara K, Yano K, Fukuda M;. Gene 1997;187:141-149.. [2]. 8529896. Sequence of the Escherichia coli C homoprotocatechuic acid. degradative operon completed with that of the. 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase-encoding gene. (hpcH).. Stringfellow JM, Turpin B, Cooper RA;. Gene 1995;166:73-76. (from Pfam)

Date:

2024-08-14

Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH. [1]. 8873595. Interaction of pyridine nucleotide substrates with Escherichia. coli dihydrodipicolinate reductase: thermodynamic and structural. analysis of binary complexes.. Reddy SG, Scapin G, Blanchard JS;. Biochemistry 1996;35:13294-13302.. [2]. 9398235. Three-dimensional structure of Escherichia coli. dihydrodipicolinate reductase in complex with NADH and the. inhibitor 2,6-pyridinedicarboxylate.. Scapin G, Reddy SG, Zheng R, Blanchard JS;. Biochemistry 1997;36:15081-15088.. [3]. 7893645. Three-dimensional structure of Escherichia coli. dihydrodipicolinate reductase.. Scapin G, Blanchard JS, Sacchettini JC;. Biochemistry 1995;34:3502-3512. (from Pfam)

Date:

2024-08-14

This domain is found in chorismate pyruvate-lyases (EC:4.1.3.40, also known as 4-HB synthase and p-hydroxybenzoic acid synthase) such as those found in Mycobacterium tuberculosis where it removes the pyruvyl group from chorismate to provide 4-hydroxybenzoate (4HB) [1]. The chorismate pyruvate-lyase encoded by sll1797 in cyanobacteria Synechocystis sp. , has been shown to catalyse the initial and essential step in plastoquinone biosynthesis [2]. In E. coli, the chorismate lyase (UbiC) catalyses the conversion of chorismate to p-hydroxybenzoate and pyruvate in the biosynthesis of ubiquinone as well [3]. [1]. 16210318. p-Hydroxybenzoic acid synthesis in Mycobacterium tuberculosis.. Stadthagen G, Kordulakova J, Griffin R, Constant P, Bottova I,. Barilone N, Gicquel B, Daffe M, Jackson M;. J Biol Chem. 2005;280:40699-40706.. [2]. 24337576. Chorismate pyruvate-lyase and 4-hydroxy-3-solanesylbenzoate. decarboxylase are required for plastoquinone biosynthesis in the. cyanobacterium Synechocystis sp. PCC6803.. Pfaff C, Glindemann N, Gruber J, Frentzen M, Sadre R;. J Biol Chem. 2014;289:2675-2686.. [3]. 20437231. Functional analysis of genes for benzoate metabolism in the. albicidin biosynthetic region of Xanthomonas albilineans.. Hashimi SM, Birch RG;. Appl Microbiol Biotechnol. 2010;87:1475-1485. (from Pfam)

Date:

2024-08-14

This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle [1]. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to liver cirrhosis, hepatocellular carcinoma, renal tubular damages and neurologic crises amongst other symptoms [1]. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites [3]. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED. The final products of this pathway are pyruvic acid and succinic semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase encoded by mhpD in E. coli Swiss:P77608 is involved in the phenylpropionic acid pathway of E. coli and catalyses the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor [5]. OHED hydratase encoded by hpcG in E. coli Swiss:P42270 is involved in the homoprotocatechuic acid (HPC) catabolism [6]. XylI in P. putida Swiss:P49155 is a 4-Oxalocrotonate decarboxylase [7]. [1]. 9101289. Mutations in th. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate aldolase (KDPG-aldolase) (from Pfam)

Date:

2024-08-14

Gene:

mhpE

Date:

2023-09-21

CloR and NovR are closely related non-heme iron proteins encoded in biosynthetic gene clusters for clorobiocin and novobiocin, respectively. Each is responsible for catalyzing two consecutive oxidative decarboxylation steps.

Gene:

cloR

Date:

2024-03-15

Gene:

aphG

Date:

2024-05-07

Gene:

bphI

Date:

2024-05-07

Gene:

tesG

Date:

2024-05-07

flavodoxin/ferredoxin-dependent (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate, part of an alternative non-mevalonate pathway for isoprenoid biosynthesis

Date:

2023-03-01

4-hydroxy-tetrahydrodipicolinate reductase catalyzes the NAD(P)-dependent conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate in amino acid biosynthesis pathways

Date:

2023-02-17

fumarylacetoacetate (FAA) hydrolase family protein belongs to the FAA hydrolase family which includes a large variety of metabolic enzymes, such as those with hydrolase functions involved in the breakdown of aromatic compounds, oxaloacetate decarboxylase, and enzymes associated with other catabolic pathways including decarboxylation of substrates other than oxaloacetate, hydration, isomerization and hydroxylation reactions

Date:

2022-07-28

UbiD family decarboxylase may catalyze the reversible decarboxylation of aromatic carboxylic acids

Date:

2022-10-25

aldolase/citrate lyase/malate synthase family protein; similar to 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) aldolase (HpcH/HpaI) that catalyzes the reversible retro-aldol cleavage of HKHD to pyruvate and succinic semialdehyde, and to malate synthase that catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA, which hydrolyzes to malate and CoA, in the glyoxylate cycle

Date:

2022-01-31