SitesBLAST
Comparing WP_013092629.1 NCBI__GCF_000092885.1:WP_013092629.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.
Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures
Found 20 (the maximum) hits to proteins with known functional sites (download)
5m3zA Crystal structure of citrobacter freundii methionine gamma-lyase with c115h replacement in the complex with l-norleucine (see paper)
35% identity, 99% coverage: 5:412/413 of query aligns to 6:394/395 of 5m3zA
- active site: R58 (= R58), Y111 (≠ F111), D183 (= D182), K208 (= K207)
- binding norleucine: Y111 (≠ F111), H113 (≠ N113), K208 (= K207), V336 (≠ T354), S337 (≠ G355)
- binding pyridoxal-5'-phosphate: G86 (= G86), I87 (≠ M87), Y111 (≠ F111), E154 (= E153), D183 (= D182), T185 (= T184), S205 (= S204), T207 (= T206), K208 (= K207)
- binding 2-[o-phosphonopyridoxyl]-amino-hexanoic acid: G86 (= G86), I87 (≠ M87), Y111 (≠ F111), D183 (= D182), S205 (= S204), T207 (= T206), K208 (= K207), V336 (≠ T354), S337 (≠ G355), R372 (= R390)
4omaA The crystal structure of methionine gamma-lyase from citrobacter freundii in complex with l-cycloserine pyridoxal-5'-phosphate (see paper)
35% identity, 99% coverage: 5:412/413 of query aligns to 7:395/396 of 4omaA
- active site: R59 (= R58), Y112 (≠ F111), D184 (= D182), K209 (= K207)
- binding [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate: G87 (= G86), I88 (≠ M87), Y112 (≠ F111), D184 (= D182), S206 (= S204), T208 (= T206), K209 (= K207), V337 (≠ T354), S338 (≠ G355), R373 (= R390)
3jwbA Crystal structure of l-methionine gamma-lyase from citrobacter freundii with norleucine (see paper)
35% identity, 99% coverage: 5:412/413 of query aligns to 7:395/396 of 3jwbA
3jwaA Crystal structure of l-methionine gamma-lyase from citrobacter freundii with methionine phosphinate (see paper)
35% identity, 99% coverage: 5:412/413 of query aligns to 7:395/396 of 3jwaA
3jw9A Crystal structure of l-methionine gamma-lyase from citrobacter freundii with s-ethyl-cysteine (see paper)
35% identity, 99% coverage: 5:412/413 of query aligns to 7:395/396 of 3jw9A
6egrA Crystal structure of citrobacter freundii methionine gamma-lyase with v358y replacement (see paper)
35% identity, 99% coverage: 5:412/413 of query aligns to 7:395/396 of 6egrA
4hf8A Crystal structure of l-methionine gamma-lyase from citrobacter freundii with glycine (see paper)
35% identity, 99% coverage: 5:412/413 of query aligns to 7:395/396 of 4hf8A
- active site: R59 (= R58), Y112 (≠ F111), D184 (= D182), K209 (= K207)
- binding n-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane]: G87 (= G86), I88 (≠ M87), Y112 (≠ F111), E155 (= E153), N159 (= N157), D184 (= D182), S206 (= S204), K209 (= K207), S338 (≠ G355), R373 (= R390)
5dx5A Crystal structure of methionine gamma-lyase from clostridium sporogenes (see paper)
36% identity, 100% coverage: 1:411/413 of query aligns to 3:396/399 of 5dx5A
- active site: R59 (= R58), Y112 (≠ F111), D186 (= D182), K211 (= K207)
- binding pyridoxal-5'-phosphate: Y57 (= Y56), R59 (= R58), S86 (≠ T85), G87 (= G86), M88 (= M87), Y112 (≠ F111), D186 (= D182), F189 (≠ I185), S208 (= S204), T210 (= T206), K211 (= K207)
3mkjA Methionine gamma-lyase from citrobacter freundii with pyridoximine-5'- phosphate (see paper)
35% identity, 99% coverage: 5:412/413 of query aligns to 7:384/386 of 3mkjA
- active site: Y101 (≠ F111), D173 (= D182), K198 (= K207)
- binding [5-hydroxy-4-(iminomethyl)-6-methyl-pyridin-3-yl]methyl dihydrogen phosphate: G76 (= G86), I77 (≠ M87), Y101 (≠ F111), E144 (= E153), D173 (= D182), F176 (≠ I185), S195 (= S204), T197 (= T206), K198 (= K207)
3vk3A Crystal structure of l-methionine gamma-lyase from pseudomonas putida c116h mutant complexed with l-methionine (see paper)
36% identity, 99% coverage: 5:413/413 of query aligns to 8:397/397 of 3vk3A
5x30C Crystal structure of pseudomonas putida methionine gamma-lyase c116h mutant with l-homocysteine intermediates. (see paper)
36% identity, 99% coverage: 5:413/413 of query aligns to 4:393/393 of 5x30C
7kb1C Complex of o-acety-l-homoserine aminocarboxypropyltransferase (mety) from thermotoga maritima and a key reaction intermediate (see paper)
33% identity, 99% coverage: 3:410/413 of query aligns to 4:424/428 of 7kb1C
- binding pyridoxal-5'-phosphate: Y57 (= Y56), R59 (= R58)
- binding (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid: G87 (= G86), Q88 (≠ M87), Y112 (≠ F111), N160 (= N157), D185 (= D182), S206 (= S204), T208 (= T206), K209 (= K207), N369 (≠ G355), I370 (≠ L356), R404 (= R390)
7kb1A Complex of o-acety-l-homoserine aminocarboxypropyltransferase (mety) from thermotoga maritima and a key reaction intermediate (see paper)
33% identity, 99% coverage: 3:410/413 of query aligns to 4:424/428 of 7kb1A
- binding (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid: Y57 (= Y56), R59 (= R58), G87 (= G86), Q88 (≠ M87), Y112 (≠ F111), N160 (= N157), D185 (= D182), S206 (= S204), T208 (= T206), K209 (= K207), N369 (≠ G355), I370 (≠ L356), R404 (= R390)
3aeoA Reaction intermediate structure of entamoeba histolytica methionine gamma-lyase 1 containing methionine alpha, beta-enamine-pyridoxamine- 5'-phosphate
34% identity, 99% coverage: 4:411/413 of query aligns to 2:386/387 of 3aeoA
- binding (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-(methylsulfanyl)but-2-enoic acid: Y51 (= Y56), R53 (= R58), G81 (= G86), M82 (= M87), Y106 (≠ F111), E149 (= E153), N153 (= N157), D178 (= D182), S200 (= S204), S202 (≠ T206), K203 (= K207), V329 (≠ T354), S330 (≠ G355), T345 (≠ F371), R365 (= R390)
3aelA Reaction intermediate structure of entamoeba histolytica methionine gamma-lyase 1 containing methionine imine-pyridoxamine-5'-phosphate and alpha-amino-alpha, beta-butenoic acid-pyridoxal-5'-phosphate
34% identity, 99% coverage: 4:411/413 of query aligns to 2:386/387 of 3aelA
- binding (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid: Y51 (= Y56), R53 (= R58)
- binding (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid: G81 (= G86), M82 (= M87), Y106 (≠ F111), E149 (= E153), N153 (= N157), D178 (= D182), T180 (= T184), S200 (= S204), S202 (≠ T206), K203 (= K207), S330 (≠ G355), T345 (≠ F371), R365 (= R390)
3aejC Reaction intermediate structure of entamoeba histolytica methionine gamma-lyase 1 tetramer containing michaelis complex and methionine- pyridoxal-5'-phosphate
34% identity, 99% coverage: 4:411/413 of query aligns to 2:386/387 of 3aejC
- active site: R53 (= R58), Y106 (≠ F111), D178 (= D182), K203 (= K207)
- binding n-[(3-hydroxy-2-methyl-5-{[(trihydroxyphosphoranyl)oxy]methyl}pyridin-4-yl)methylene]methionine: F42 (= F46), Y51 (= Y56), R53 (= R58)
- binding methionine: Y106 (≠ F111), K203 (= K207), S330 (≠ G355), L331 (= L356), T345 (≠ F371), R365 (= R390)
3aejA Reaction intermediate structure of entamoeba histolytica methionine gamma-lyase 1 tetramer containing michaelis complex and methionine- pyridoxal-5'-phosphate
34% identity, 99% coverage: 4:411/413 of query aligns to 2:386/387 of 3aejA
- binding n-[(3-hydroxy-2-methyl-5-{[(trihydroxyphosphoranyl)oxy]methyl}pyridin-4-yl)methylene]methionine: Y51 (= Y56), R53 (= R58), G81 (= G86), M82 (= M87), Y106 (≠ F111), E149 (= E153), N153 (= N157), D178 (= D182), S200 (= S204), S202 (≠ T206), K203 (= K207), S330 (≠ G355), L331 (= L356), T345 (≠ F371), R365 (= R390)
1pg8A Crystal structure of l-methionine alpha-, gamma-lyase
36% identity, 99% coverage: 5:413/413 of query aligns to 9:398/398 of 1pg8A
- active site: R61 (= R58), Y114 (≠ F111), D186 (= D182), K211 (= K207)
- binding pyridoxal-5'-phosphate: Y59 (= Y56), R61 (= R58), S88 (≠ T85), G89 (= G86), M90 (= M87), Y114 (≠ F111), D186 (= D182), S208 (= S204), T210 (= T206), K211 (= K207)
P13254 L-methionine gamma-lyase; MGL; Homocysteine desulfhydrase; L-methioninase; EC 4.4.1.11; EC 4.4.1.2 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 3 papers)
36% identity, 99% coverage: 5:413/413 of query aligns to 9:398/398 of P13254
- YSR 59:61 (≠ YAR 56:58) binding pyridoxal 5'-phosphate
- R61 (= R58) mutation R->A,E,F: Loss of elimination activity against L-methionine.
- GM 89:90 (= GM 86:87) binding in other chain
- Y114 (≠ F111) binding substrate
- C116 (≠ N113) mutation to H: Drastic decrease of the catalytic efficiency of the elimination reaction with L-methionine, by 6700-fold, and increases that with L-cysteine by 7-fold, mainly due to changes in kcat. Loss of ability to catalyze replacement reaction between L-methionine and 2-mercaptoethanol.; mutation to S: 9% of wild-type elimination activity against L-methionine.; mutation to T: 40% of wild-type elimination activity against L-methionine.
- SAT 208:210 (≠ SLT 204:206) binding in other chain
- K211 (= K207) modified: N6-(pyridoxal phosphate)lysine
- K240 (≠ R257) mutation K->D,E: Marked decrease in elimination activity against both L-methionine and DL-homocysteine.; mutation to M: 50% reduction in alpha,gamma-elimination activity against DL-homocysteine, while retaining elimination activity against L-methionine and L-cysteine.
- D241 (= D258) mutation D->H,R: 5 to 14-fold reduction in alpha,gamma-elimination activity against L-methionine, while no change in affinity for L-methionine.
- R375 (= R390) binding substrate
5x2xA Crystal structure of pseudomonas putida methionine gamma-lyase wild type with l-homocysteine intermediates (see paper)
36% identity, 99% coverage: 5:413/413 of query aligns to 3:392/392 of 5x2xA
- active site: R55 (= R58), Y108 (≠ F111), D180 (= D182), K205 (= K207)
- binding (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid: Y53 (= Y56), R55 (= R58), G83 (= G86), M84 (= M87), Y108 (≠ F111), N155 (= N157), D180 (= D182), S202 (= S204), T204 (= T206), K205 (= K207), V333 (≠ T354), S334 (≠ G355), R369 (= R390)
Query Sequence
>WP_013092629.1 NCBI__GCF_000092885.1:WP_013092629.1
MDKQGFTTGIVHGDRTAGTEHGALRQPVHTSVQYGFERVEDLIGVFQGTKKGGFNYARQG
TPTTAALERKITSLEEGVGTVCFSTGMAGITATFLTLLRAGDHLVSSRYVFGNTNSLFGT
LRALGVEVTTVDACRLDDVKNAIRPNTRMVFVETIANPGTQIPDLQGIGDVCRERGIAYV
VDNTITSPALFKPKAVGASLVINSLTKTIAGHGAALGGAVTDTGLFDWSAYPNIADDYRR
SGAKDQGLLQIRKKGLRDMGASLSSEQAHSIAMGAETLALRVRQSSDNALALAQFLEGHE
AIGKVFYPGLKSHPQYDIAQTLFKGASWLLSFELLNVDRMIEVVNALKLPVKATGLGDTR
TLIIPVAPTIFFEAGPETRKAMGISDGMLRLSAGIEDIDDLIADFAQALKLAA
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SitesBLAST's Database
SitesBLAST's database includes
(1) SwissProt
entries with experimentally-supported functional features;
and (2) protein structures with bound ligands, from the
BioLip database.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory