The Enzyme Database

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EC 1.4.3.22     
Accepted name: diamine oxidase
Reaction: histamine + H2O + O2 = (imidazol-4-yl)acetaldehyde + NH3 + H2O2
Other name(s): amine oxidase (ambiguous); amine oxidase (copper-containing) (ambiguous); CAO (ambiguous); Cu-containing amine oxidase (ambiguous); copper amine oxidase (ambiguous); diamine oxidase (ambiguous); diamino oxhydrase (ambiguous); histaminase; histamine deaminase (incorrect); semicarbazide-sensitive amine oxidase (incorrect); SSAO (incorrect)
Systematic name: histamine:oxygen oxidoreductase (deaminating)
Comments: A group of enzymes that oxidize diamines, such as histamine, and also some primary monoamines but have little or no activity towards secondary and tertiary amines. They are copper quinoproteins (2,4,5-trihydroxyphenylalanine quinone) and, like EC 1.4.3.21 (primary-amine oxidase) but unlike EC 1.4.3.4 (monoamine oxidase), they are sensitive to inhibition by carbonyl-group reagents, such as semicarbazide.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zeller, E.A. Diamine oxidases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 8, Academic Press, New York, 1963, pp. 313–335.
2.  Crabbe, M.J., Waight, R.D., Bardsley, W.G., Barker, R.W., Kelly, I.D. and Knowles, P.F. Human placental diamine oxidase. Improved purification and characterization of a copper- and manganese-containing amine oxidase with novel substrate specificity. Biochem. J. 155 (1976) 679–687. [PMID: 182134]
3.  Chassande, O., Renard, S., Barbry, P. and Lazdunski, M. The human gene for diamine oxidase, an amiloride binding protein. Molecular cloning, sequencing, and characterization of the promoter. J. Biol. Chem. 269 (1994) 14484–14489. [PMID: 8182053]
4.  Houen, G. Mammalian Cu-containing amine oxidases (CAOs): new methods of analysis, structural relationships, and possible functions. APMIS Suppl. 96 (1999) 1–46. [PMID: 10668504]
5.  Elmore, B.O., Bollinger, J.A. and Dooley, D.M. Human kidney diamine oxidase: heterologous expression, purification, and characterization. J. Biol. Inorg. Chem. 7 (2002) 565–579. [DOI] [PMID: 12072962]
[EC 1.4.3.22 created 2007 (EC 1.4.3.6 created 1961, part-incorporated 2008)]
 
 
EC 1.11.1.18     
Accepted name: bromide peroxidase
Reaction: RH + HBr + H2O2 = RBr + 2 H2O
Other name(s): bromoperoxidase; haloperoxidase (ambiguous); eosinophil peroxidase
Systematic name: bromide:hydrogen-peroxide oxidoreductase
Comments: Bromoperoxidases of red and brown marine algae (Rhodophyta and Phaeophyta) contain vanadate. They catalyse the bromination of a range of organic molecules such as sesquiterpenes, forming stable C-Br bonds. Bromoperoxidases also oxidize iodides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  De Boer, E., Tromp, M.G.M., Plat, H., Krenn, G.E. and Wever, R Vanadium(v) as an essential element for haloperoxidase activity in marine brown-algae - purification and characterization of a vanadium(V)-containing bromoperoxidase from Laminaria saccharina. Biochim. Biophys. Acta 872 (1986) 104–115.
2.  Tromp, M.G., Olafsson, G., Krenn, B.E. and Wever, R. Some structural aspects of vanadium bromoperoxidase from Ascophyllum nodosum. Biochim. Biophys. Acta 1040 (1990) 192–198. [DOI] [PMID: 2400770]
3.  Isupov, M.N., Dalby, A.R., Brindley, A.A., Izumi, Y., Tanabe, T., Murshudov, G.N. and Littlechild, J.A. Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis. J. Mol. Biol. 299 (2000) 1035–1049. [DOI] [PMID: 10843856]
4.  Carter-Franklin, J.N. and Butler, A. Vanadium bromoperoxidase-catalyzed biosynthesis of halogenated marine natural products. J. Am. Chem. Soc. 126 (2004) 15060–15066. [DOI] [PMID: 15548002]
5.  Ohshiro, T., Littlechild, J., Garcia-Rodriguez, E., Isupov, M.N., Iida, Y., Kobayashi, T. and Izumi, Y. Modification of halogen specificity of a vanadium-dependent bromoperoxidase. Protein Sci. 13 (2004) 1566–1571. [DOI] [PMID: 15133166]
[EC 1.11.1.18 created 2010]
 
 
EC 2.3.2.26     
Accepted name: HECT-type E3 ubiquitin transferase
Reaction: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N6-ubiquitinyl-L-lysine (overall reaction)
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
(1b) [HECT-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [HECT-type E3 ubiquitin transferase]-L-cysteine + [acceptor protein]-N6-ubiquitinyl-L-lysine
Glossary: HECT protein domain = Homologous to the E6-AP Carboxyl Terminus protein domain
Other name(s): HECT E3 ligase (misleading); ubiquitin transferase HECT-E3; S-ubiquitinyl-[HECT-type E3-ubiquitin transferase]-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming)
Systematic name: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming)
Comments: In the first step the enzyme transfers ubiquitin from the E2 ubiquitin-conjugating enzyme (EC 2.3.2.23) to a cysteine residue in its HECT domain (which is located in the C-terminal region), forming a thioester bond. In a subsequent step the enzyme transfers the ubiquitin to an acceptor protein, resulting in the formation of an isopeptide bond between the C-terminal glycine residue of ubiquitin and the ε-amino group of an L-lysine residue of the acceptor protein. cf. EC 2.3.2.27, RING-type E3 ubiquitin transferase and EC 2.3.2.31, RBR-type E3 ubiquitin transferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Maspero, E., Mari, S., Valentini, E., Musacchio, A., Fish, A., Pasqualato, S. and Polo, S. Structure of the HECT:ubiquitin complex and its role in ubiquitin chain elongation. EMBO Rep. 12 (2011) 342–349. [DOI] [PMID: 21399620]
2.  Metzger, M.B., Hristova, V.A. and Weissman, A.M. HECT and RING finger families of E3 ubiquitin ligases at a glance. J. Cell Sci. 125 (2012) 531–537. [DOI] [PMID: 22389392]
[EC 2.3.2.26 created 2015, modified 2017]
 
 
EC 2.3.2.27     
Accepted name: RING-type E3 ubiquitin transferase
Reaction: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N6-ubiquitinyl-L-lysine
Glossary: RING = Really Interesting New Gene
Other name(s): RING E3 ligase (misleading); ubiquitin transferase RING E3; S-ubiquitinyl-[ubiquitin-conjugating E2 enzyme]-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming, RING-type)
Systematic name: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming; RING-type)
Comments: RING E3 ubiquitin transferases serve as mediators bringing the ubiquitin-charged E2 ubiquitin-conjugating enzyme (EC 2.3.2.23) and an acceptor protein together to enable the direct transfer of ubiquitin through the formation of an isopeptide bond between the C-terminal glycine residue of ubiquitin and the ε-amino group of an L-lysine residue of the acceptor protein. Unlike EC 2.3.2.26, HECT-type E3 ubiquitin transferase, the RING-E3 domain does not form a catalytic thioester intermediate with ubiquitin. Many members of the RING-type E3 ubiquitin transferase family are not able to bind a substrate directly, and form a complex with a cullin scaffold protein and a substrate recognition module (the complexes are named CRL for Cullin-RING-Ligase). In these complexes, the RING-type E3 ubiquitin transferase provides an additional function, mediating the transfer of a NEDD8 protein from a dedicated E2 carrier to the cullin protein (see EC 2.3.2.32, cullin-RING-type E3 NEDD8 transferase). cf. EC 2.3.2.31, RBR-type E3 ubiquitin transferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Eisele, F. and Wolf, D.H. Degradation of misfolded protein in the cytoplasm is mediated by the ubiquitin ligase Ubr1. FEBS Lett. 582 (2008) 4143–4146. [DOI] [PMID: 19041308]
2.  Metzger, M.B., Hristova, V.A. and Weissman, A.M. HECT and RING finger families of E3 ubiquitin ligases at a glance. J. Cell Sci. 125 (2012) 531–537. [DOI] [PMID: 22389392]
3.  Plechanovova, A., Jaffray, E.G., Tatham, M.H., Naismith, J.H. and Hay, R.T. Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis. Nature 489 (2012) 115–120. [DOI] [PMID: 22842904]
4.  Pruneda, J.N., Littlefield, P.J., Soss, S.E., Nordquist, K.A., Chazin, W.J., Brzovic, P.S. and Klevit, R.E. Structure of an E3:E2~Ub complex reveals an allosteric mechanism shared among RING/U-box ligases. Mol. Cell 47 (2012) 933–942. [DOI] [PMID: 22885007]
5.  Metzger, M.B., Pruneda, J.N., Klevit, R.E. and Weissman, A.M. RING -type E3 ligases: master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination. Biochim. Biophys. Acta 1843 (2014) 47–60. [DOI] [PMID: 23747565]
[EC 2.3.2.27 created 2015, modified 2017]
 
 
EC 2.3.2.31     
Accepted name: RBR-type E3 ubiquitin transferase
Reaction: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N6-ubiquitinyl-L-lysine (overall reaction)
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [RBR-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [RBR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
(1b) [RBR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [RBR-type E3 ubiquitin transferase]-L-cysteine + [acceptor protein]-N6-ubiquitinyl-L-lysine
Glossary: RBR = RING between RING
RING = Really Interesting New Gene
Systematic name: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming; RBR-type)
Comments: RBR-type E3 ubiquitin transferases have two RING fingers separated by an internal motif (IBR, for In Between RING). The enzyme interacts with the CRL (Cullin-RING ubiquitin Ligase) complexes formed by certain RING-type E3 ubiquitin transferase (see EC 2.3.2.27), which include a neddylated cullin scaffold protein and a substrate recognition module. The RING1 domain binds an EC 2.3.2.23, E2 ubiquitin-conjugating enzyme, and transfers the ubiquitin that is bound to it to an internal cysteine residue in the RING2 domain, followed by the transfer of the ubiquitin from RING2 to the substrate [4]. Once the substrate has been ubiquitylated by the RBR-type ligase, it can be ubiqutylated further using ubiquitin carried directly on E2 enzymes, in a reaction catalysed by EC 2.3.2.27. Activity of the RBR-type enzyme is dependent on neddylation of the cullin protein in the CRL complex [2,4]. cf. EC 2.3.2.26, HECT-type E3 ubiquitin transferase, EC 2.3.2.27, RING-type E3 ubiquitin transferase, and EC 2.3.2.32, cullin-RING-type E3 NEDD8 transferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wenzel, D.M., Lissounov, A., Brzovic, P.S. and Klevit, R.E. UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids. Nature 474 (2011) 105–108. [DOI] [PMID: 21532592]
2.  Kelsall, I.R., Duda, D.M., Olszewski, J.L., Hofmann, K., Knebel, A., Langevin, F., Wood, N., Wightman, M., Schulman, B.A. and Alpi, A.F. TRIAD1 and HHARI bind to and are activated by distinct neddylated Cullin-RING ligase complexes. EMBO J. 32 (2013) 2848–2860. [DOI] [PMID: 24076655]
3.  Duda, D.M., Olszewski, J.L., Schuermann, J.P., Kurinov, I., Miller, D.J., Nourse, A., Alpi, A.F. and Schulman, B.A. Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism. Structure 21 (2013) 1030–1041. [DOI] [PMID: 23707686]
4.  Scott, D.C., Rhee, D.Y., Duda, D.M., Kelsall, I.R., Olszewski, J.L., Paulo, J.A., de Jong, A., Ovaa, H., Alpi, A.F., Harper, J.W. and Schulman, B.A. Two distinct types of E3 ligases work in unison to regulate substrate ubiquitylation. Cell 166 (2016) 1198–1214.e24. [DOI] [PMID: 27565346]
[EC 2.3.2.31 created 2017]
 
 
EC 2.4.1.184     
Accepted name: galactolipid galactosyltransferase
Reaction: 2 a 1,2-diacyl-3-O-(β-D-galactosyl)-sn-glycerol = a 1,2-diacyl-3-O-[β-D-galactosyl-(1→6)-β-D-galactosyl]-sn-glycerol + a 1,2-diacyl-sn-glycerol
For diagram of galactosyl diacylglycerol, click here
Glossary: a 1,2-diacyl-3-O-(β-D-galactosyl)-sn-glycerol = monogalactosyldiacylglycerol
Other name(s): galactolipid-galactolipid galactosyltransferase; galactolipid:galactolipid galactosyltransferase; interlipid galactosyltransferase; GGGT; DGDG synthase (ambiguous); digalactosyldiacylglycerol synthase (ambiguous); 3-(β-D-galactosyl)-1,2-diacyl-sn-glycerol:mono-3-(β-D-galactosyl)-1,2-diacyl-sn-glycerol β-D-galactosyltransferase; 3-(β-D-galactosyl)-1,2-diacyl-sn-glycerol:3-(β-D-galactosyl)-1,2-diacyl-sn-glycerol β-D-galactosyltransferase; SFR2 (gene name)
Systematic name: 1,2-diacyl-3-O-(β-D-galactosyl)-sn-glycerol:1,2-diacyl-3-O-(β-D-galactosyl)-sn-glycerol β-D-galactosyltransferase
Comments: The enzyme converts monogalactosyldiacylglycerol to digalactosyldiacylglycerol, trigalactosyldiacylglycerol and tetragalactosyldiacylglycerol. All residues are connected by β linkages. The activity is localized to chloroplast envelope membranes, but it does not contribute to net galactolipid synthesis in plants, which is performed by EC 2.4.1.46, monogalactosyldiacylglycerol synthase, and EC 2.4.1.241, digalactosyldiacylglycerol synthase. Note that the β,β-digalactosyldiacylglycerol formed by this enzyme is different from the more common α,β-digalactosyldiacylglycerol formed by EC 2.4.1.241. The enzyme provides an important mechanism for the stabilization of the chloroplast membranes during freezing and drought stress.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 66676-74-2
References:
1.  Dorne, A.-J., Block, M.A., Joyard, J. and Douce, R. The galactolipid-galactolipid galactosyltransferase is located on the outer surface of the outer-membrane of the chloroplast envelope. FEBS Lett. 145 (1982) 30–34.
2.  Heemskerk, J.W.M., Wintermans, J.F.G.M., Joyard, J., Block, M.A., Dorne, A.-J. and Douce, R. Localization of galactolipid:galactolipid galactosyltransferase and acyltransferase in outer envelope membrane of spinach chloroplasts. Biochim. Biophys. Acta 877 (1986) 281–289.
3.  Heemskerk, J.W.M., Jacobs, F.H.H. and Wintermans, J.F.G.M. UDPgalactose-independent synthesis of monogalactosyldiacylglycerol. An enzymatic activity of the spinach chloroplast envelope. Biochim. Biophys. Acta 961 (1988) 38–47. [DOI]
4.  Kelly, A.A., Froehlich, J.E. and Dörmann, P. Disruption of the two digalactosyldiacylglycerol synthase genes DGD1 and DGD2 in Arabidopsis reveals the existence of an additional enzyme of galactolipid synthesis. Plant Cell 15 (2003) 2694–2706. [DOI] [PMID: 14600212]
5.  Benning, C. and Ohta, H. Three enzyme systems for galactoglycerolipid biosynthesis are coordinately regulated in plants. J. Biol. Chem. 280 (2005) 2397–2400. [DOI] [PMID: 15590685]
6.  Fourrier, N., Bedard, J., Lopez-Juez, E., Barbrook, A., Bowyer, J., Jarvis, P., Warren, G. and Thorlby, G. A role for SENSITIVE TO FREEZING2 in protecting chloroplasts against freeze-induced damage in Arabidopsis. Plant J. 55 (2008) 734–745. [DOI] [PMID: 18466306]
7.  Moellering, E.R., Muthan, B. and Benning, C. Freezing tolerance in plants requires lipid remodeling at the outer chloroplast membrane. Science 330 (2010) 226–228. [DOI] [PMID: 20798281]
[EC 2.4.1.184 created 1990, modified 2005, modified 2015]
 
 
EC 3.2.1.132     
Accepted name: chitosanase
Reaction: Endohydrolysis of β-(1→4)-linkages between D-glucosamine residues in a partly acetylated chitosan
Systematic name: chitosan N-acetylglucosaminohydrolase
Comments: A whole spectrum of chitosanases are now known (for more details, see rbrzezinski.recherche.usherbrooke.ca/">http://rbrzezinski.recherche.usherbrooke.ca/). They can hydrolyse various types of links in chitosan. The only constant property is the endohydrolysis of GlcN-GlcN links, which is common to all known chitosanases. One known chitosanase is limited to this link recognition [4], while the majority can also recognize GlcN-GlcNAc links or GlcNAc-GlcN links but not both. They also do not recognize GlcNAc-GlcNAc links in partly acetylated chitosan.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 51570-20-8
References:
1.  Fenton, D.M. and Eveleigh, D.E. Purification and mode of action of a chitosanase from Penicillium islandicum. J. Gen. Microbiol. 126 (1981) 151–165.
2.  Saito, J.-I., Kita, A., Higuchi, Y., Nagata, Y., Ando, A. and Miki, K. Crystal structure of chitosanase from Bacillus circulans MH-K1 at 1.6-Å resolution and its substrate recognition mechanism. J. Biol. Chem. 274 (1999) 30818–30825. [DOI] [PMID: 10521473]
3.  Izume, M., Nagae, S., Kawagishi, H., Mitsutomi, M. and Ohtakara, A. Action pattern of Bacillus sp. No. 7-M chitosanase on partially N-acetylated chitosan. Biosci. Biotechnol. Biochem. 56 (1992) 448–453. [DOI] [PMID: 1368330]
4.  Marcotte, E.M., Monzingo, A.F., Ernst, S.R., Brzezinski, R. and Robertus, J.D. X-ray structure of an anti-fungal chitosanase from Streptomyces N174. Nat. Struct. Biol. 3 (1996) 155–162. [PMID: 8564542]
[EC 3.2.1.132 created 1990, modified 2004]
 
 
EC 3.4.21.89     
Accepted name: signal peptidase I
Reaction: Cleavage of hydrophobic, N-terminal signal or leader sequences
Other name(s): leader peptidase I; signal proteinase; Escherichia coli leader peptidase; eukaryotic signal peptidase; eukaryotic signal proteinase; leader peptidase; leader peptide hydrolase; leader proteinase; signal peptidase; pilin leader peptidase; SPC; prokaryotic signal peptidase; prokaryotic leader peptidase; HOSP; prokaryotic signal proteinase; propeptidase; PuIO prepilin peptidase; signal peptide hydrolase; signal peptide peptidase; signalase; bacterial leader peptidase 1; pilin leader peptidase
Comments: The enzyme is found in bacterial membranes and in chloroplast thylakoid membranes. Unaffected by inhibitors of most serine peptidases, but site-directed mutagenesis implicates a Ser/Lys catalytic dyad in activity [1,3]. Hydrolyses a single bond -Ala┼Ala- in M13 phage procoat protein, producing free signal peptide and coat protein. Formerly included in EC 3.4.99.36. Eukaryote signal peptidases that may have somewhat different specificity are known from the endoplasmic reticulum membrane [4] and mitochondrial inner membrane [2]. Type example of peptidase family S26
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, MEROPS, PDB, CAS registry number: 65979-36-4
References:
1.  Black, M.T. Evidence that the catalytic activity of prokaryote leader peptidase depends upon the operation of a serine-lysine catalytic dyad. J. Bacteriol. 175 (1993) 4957–4961. [DOI] [PMID: 8394311]
2.  Nunnari, J., Fox, T.D. and Walter, P. A mitochondrial protease with two catalytic subunits of nonoverlapping specificities. Science 262 (1993) 1997–2004. [DOI] [PMID: 8266095]
3.  Tschantz, W.R., Sung, M., Delgado-Partin, V.M. and Dalbey, R.E. A serine and a lysine residue implicated in the catalytic mechanism of the Escherichia coli leader peptidase. J. Biol. Chem. 268 (1993) 27349–27354. [PMID: 8262975]
4.  Lively, M.O., Newsome, A.L. and Nusier, M. Eukaryote microsomal signal peptidases. Methods Enzymol. 244 (1994) 301–314. [DOI] [PMID: 7845216]
5.  Tschantz, W.R. and Dalbey, R.E. Bacterial leader peptidase I. Methods Enzymol. 244 (1994) 285–301. [DOI] [PMID: 7845215]
6.  Chaal, B.K., Mould, R.M., Barbrook, A.C., Gray, J.C. and Howe, C.J. Characterization of a cDNA encoding the thylakoidal processing peptidase from Arabidopsis thaliana. Implications for the origin and catalytic mechanism of the enzyme. J. Biol. Chem. 273 (1998) 689–692. [DOI] [PMID: 9422718]
7.  Inoue, K., Baldwin, A.J., Shipman, R.L., Matsui, K., Theg, S.M. and Ohme-Takagi, M. Complete maturation of the plastid protein translocation channel requires a type I signal peptidase. J. Cell Biol. 171 (2005) 425–430. [DOI] [PMID: 16275749]
[EC 3.4.21.89 created 1984 as EC 3.4.99.36, transferred 1995 to EC 3.4.21.89]
 
 


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