SitesBLAST
Comparing GFF2427 PGA1_c24580 putative serine hydroxymethyltransferase 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)
4uqvG Methanococcus jannaschii serine hydroxymethyl-transferase in complex with plp (see paper)
32% identity, 88% coverage: 50:433/435 of query aligns to 23:415/429 of 4uqvG
- active site: Y50 (≠ P77), E52 (≠ L79), D196 (= D223), S223 (= S250), K226 (= K253), Q232 (≠ A259)
- binding pyridoxal-5'-phosphate: G93 (= G120), V94 (≠ A121), H121 (= H148), A198 (= A225), H199 (= H226), S223 (= S250), H225 (≠ Y252), K226 (= K253)
4bhdB Methanococcus jannaschii serine hydroxymethyl-transferase, apo form (see paper)
32% identity, 80% coverage: 88:433/435 of query aligns to 46:381/395 of 4bhdB
Sites not aligning to the query:
Q5SI56 Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
31% identity, 86% coverage: 40:412/435 of query aligns to 17:385/407 of Q5SI56
- Y51 (≠ P77) binding
- GS 94:95 (≠ GA 120:121) binding
- S172 (= S198) binding
- H200 (= H226) binding
- H225 (≠ Y252) binding
- K226 (= K253) modified: N6-(pyridoxal phosphate)lysine
- G258 (≠ N285) binding
8suiB Joint x-ray/neutron structure of thermus thermophilus serine hydroxymethyltransferase (tthshmt) in internal aldimine state with l- ser bound in a pre-michalis complex (see paper)
31% identity, 86% coverage: 40:412/435 of query aligns to 12:380/402 of 8suiB
8ssyA Room-temperature x-ray structure of thermus thermophilus serine hydroxymethyltransferase (shmt) bound with d-ser in a pseudo- michaelis complex (see paper)
31% identity, 86% coverage: 40:412/435 of query aligns to 12:380/402 of 8ssyA
2dkjA Crystal structure of t.Th.Hb8 serine hydroxymethyltransferase
31% identity, 86% coverage: 40:412/435 of query aligns to 12:380/402 of 2dkjA
- active site: Y46 (≠ P77), E48 (≠ L79), D192 (= D223), T218 (≠ S250), K221 (= K253), R227 (≠ A259)
- binding pyridoxal-5'-phosphate: S88 (= S119), G89 (= G120), S90 (≠ A121), H117 (= H148), S167 (= S198), D192 (= D223), A194 (= A225), H220 (≠ Y252), K221 (= K253)
6ymfA Crystal structure of serine hydroxymethyltransferase from aphanothece halophytica in the plp-serine external aldimine state (see paper)
30% identity, 86% coverage: 57:428/435 of query aligns to 34:411/418 of 6ymfA
- active site: Y54 (≠ P77), E56 (≠ L79), D200 (= D223), T226 (≠ S250), K229 (= K253), R235 (≠ A259)
- binding [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine: S34 (≠ A57), S96 (= S119), G97 (= G120), A98 (= A121), H125 (= H148), S175 (= S198), D200 (= D223), A202 (= A225), H203 (= H226), T226 (≠ S250), K229 (= K253), R361 (= R385)
6ymdA Crystal structure of serine hydroxymethyltransferase from aphanothece halophytica in the covalent complex with malonate (see paper)
30% identity, 86% coverage: 57:428/435 of query aligns to 34:411/420 of 6ymdA
- active site: Y54 (≠ P77), E56 (≠ L79), D200 (= D223), T226 (≠ S250), K229 (= K253), R235 (≠ A259)
- binding malonate ion: S34 (≠ A57), Y54 (≠ P77), E56 (≠ L79), Y64 (≠ E87), H125 (= H148), H203 (= H226), K229 (= K253), R361 (= R385)
- binding 4'-deoxy-4'-aminopyridoxal-5'-phosphate: Y54 (≠ P77), S96 (= S119), G97 (= G120), A98 (= A121), H125 (= H148), Y174 (≠ G197), S175 (= S198), D200 (= D223), A202 (= A225), T226 (≠ S250), K229 (= K253), G261 (vs. gap)
2vmyA Crystal structure of f351gbsshmt in complex with gly and fthf (see paper)
31% identity, 79% coverage: 71:413/435 of query aligns to 45:385/405 of 2vmyA
- active site: Y51 (≠ P77), E53 (≠ L79), D197 (= D223), T223 (≠ S250), K226 (= K253), R232 (≠ A259)
- binding N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid: E53 (≠ L79), Y60 (= Y86), Y61 (≠ E87), L117 (≠ A143), G121 (= G147), H122 (= H148), L123 (≠ V149), S172 (= S198), K248 (≠ S276), F251 (= F279), N341 (≠ I370), S349 (≠ V377), P350 (≠ E378), G351 (= G379), R357 (= R385)
- binding glycine: Y51 (≠ P77), Y61 (≠ E87), H200 (= H226), K226 (= K253), R357 (= R385)
- binding pyridoxal-5'-phosphate: Y51 (≠ P77), S93 (= S119), G94 (= G120), A95 (= A121), H122 (= H148), S172 (= S198), D197 (= D223), A199 (= A225), H200 (= H226), T223 (≠ S250), K226 (= K253), G257 (≠ N285)
Sites not aligning to the query:
2vmxA Crystal structure of f351gbsshmt in complex with l-allo-thr (see paper)
31% identity, 79% coverage: 71:413/435 of query aligns to 45:385/405 of 2vmxA
- active site: Y51 (≠ P77), E53 (≠ L79), D197 (= D223), T223 (≠ S250), K226 (= K253), R232 (≠ A259)
- binding allo-threonine: H122 (= H148), H200 (= H226), R357 (= R385)
- binding pyridoxal-5'-phosphate: S93 (= S119), G94 (= G120), A95 (= A121), H122 (= H148), S172 (= S198), D197 (= D223), A199 (= A225), H200 (= H226), T223 (≠ S250), K226 (= K253)
Sites not aligning to the query:
6ti4A Shmt from streptococcus thermophilus tyr55ser variant in complex with plp/d-serine/lys230 gem diamine complex
29% identity, 86% coverage: 48:421/435 of query aligns to 20:396/410 of 6ti4A
- active site: S49 (≠ P77), E51 (≠ L79), D195 (= D223), T221 (≠ S250), K224 (= K253), R230 (≠ A259)
- binding magnesium ion: A50 (≠ S78), E51 (≠ L79), Y58 (= Y86), Y59 (≠ E87)
- binding (2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid: E51 (≠ L79), Y59 (≠ E87), S91 (= S119), G92 (= G120), S93 (≠ A121), H120 (= H148), S170 (= S198), D195 (= D223), A197 (= A225), H198 (= H226), K224 (= K253), G255 (≠ A284), R357 (= R385)
6ti3A Apo-shmt from streptococcus thermophilus tyr55ser variant in complex with d-threonine
29% identity, 86% coverage: 48:421/435 of query aligns to 20:396/410 of 6ti3A
- active site: S49 (≠ P77), E51 (≠ L79), D195 (= D223), T221 (≠ S250), K224 (= K253), R230 (≠ A259)
- binding d-threonine: S91 (= S119), G92 (= G120), S93 (≠ A121), H223 (≠ Y252), G255 (≠ A284), G256 (≠ N285)
6tghC Shmt from streptococcus thermophilus tyr55thr variant in complex with d-serine both as external aldimine and as non-covalent complex
29% identity, 86% coverage: 48:421/435 of query aligns to 20:396/410 of 6tghC
- active site: T49 (≠ P77), E51 (≠ L79), D195 (= D223), T221 (≠ S250), K224 (= K253), R230 (≠ A259)
- binding d-serine: S29 (≠ A57), H198 (= H226), R357 (= R385)
- binding L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene]: E51 (≠ L79), G255 (≠ A284)
- binding pyridoxal-5'-phosphate: S91 (= S119), G92 (= G120), S93 (≠ A121), H120 (= H148), D195 (= D223), A197 (= A225), H198 (= H226), T221 (≠ S250), K224 (= K253)
6tghA Shmt from streptococcus thermophilus tyr55thr variant in complex with d-serine both as external aldimine and as non-covalent complex
29% identity, 86% coverage: 48:421/435 of query aligns to 20:396/410 of 6tghA
- active site: T49 (≠ P77), E51 (≠ L79), D195 (= D223), T221 (≠ S250), K224 (= K253), R230 (≠ A259)
- binding d-serine: E51 (≠ L79), Y59 (≠ E87)
- binding L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene]: S29 (≠ A57), S91 (= S119), G92 (= G120), S93 (≠ A121), H120 (= H148), S170 (= S198), D195 (= D223), A197 (= A225), H198 (= H226), K224 (= K253), R357 (= R385)
7x5nA Crystal structure of e. Faecium shmt in complex with (+)-shin-1 and plp-ser (see paper)
30% identity, 89% coverage: 41:428/435 of query aligns to 16:403/409 of 7x5nA
- binding (4R)-6-azanyl-4-[3-(hydroxymethyl)-5-phenyl-phenyl]-3-methyl-4-propan-2-yl-1H-pyrano[2,3-c]pyrazole-5-carbonitrile: E51 (≠ L79), Y58 (= Y86), Y59 (≠ E87), L115 (≠ A143), G119 (= G147), H120 (= H148), L121 (≠ V149), K340 (≠ G369), N341 (≠ I370), S342 (≠ G371), P350 (≠ G379), F351 (vs. gap), R357 (= R385)
- binding [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine: S29 (≠ A57), Y49 (≠ P77), E51 (≠ L79), Y59 (≠ E87), S91 (= S119), G92 (= G120), S93 (≠ A121), H120 (= H148), S170 (= S198), D195 (= D223), A197 (= A225), H198 (= H226), K224 (= K253), R357 (= R385)
7v3dA Complex structure of serine hydroxymethyltransferase from enterococcus faecium and its inhibitor (see paper)
30% identity, 89% coverage: 41:428/435 of query aligns to 16:403/409 of 7v3dA
- binding (4R)-6-azanyl-4-[3-(hydroxymethyl)-5-phenyl-phenyl]-3-methyl-4-propan-2-yl-1H-pyrano[2,3-c]pyrazole-5-carbonitrile: E51 (≠ L79), Y58 (= Y86), L115 (≠ A143), G119 (= G147), H120 (= H148), L121 (≠ V149), K340 (≠ G369), S342 (≠ G371), P350 (≠ G379), F351 (vs. gap), R357 (= R385)
- binding pyridoxal-5'-phosphate: Y49 (≠ P77), S91 (= S119), G92 (= G120), S93 (≠ A121), H120 (= H148), S170 (= S198), D195 (= D223), A197 (= A225), K224 (= K253), G255 (≠ A284)
7x5oB Crystal structure of e. Faecium shmt in complex with me-thf and plp- gly (see paper)
30% identity, 89% coverage: 41:428/435 of query aligns to 17:404/412 of 7x5oB
- binding n-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane]: S30 (≠ A57), Y50 (≠ P77), Y60 (≠ E87), S92 (= S119), G93 (= G120), S94 (≠ A121), H121 (= H148), S171 (= S198), D196 (= D223), A198 (= A225), H199 (= H226), K225 (= K253), R358 (= R385)
- binding n-[4-({[(6s)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-l-glutamic acid: E52 (≠ L79), Y59 (= Y86), L116 (≠ A143), G119 (= G146), G120 (= G147), H121 (= H148), S171 (= S198), P252 (= P280), N342 (≠ I370), P351 (≠ G379)
4wxgA Crystal structure of l-serine hydroxymethyltransferase in complex with a mixture of l-threonine and glycine (see paper)
29% identity, 86% coverage: 48:421/435 of query aligns to 20:396/410 of 4wxgA
- active site: T43 (≠ S71), L45 (= L73), G189 (= G217), A215 (= A244), T218 (≠ M247), R230 (≠ A259)
- binding N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine: S29 (≠ A57), Y49 (≠ P77), E51 (≠ L79), Y59 (≠ E87), S91 (= S119), G92 (= G120), S93 (≠ A121), H120 (= H148), S170 (= S198), D195 (= D223), A197 (= A225), H198 (= H226), T221 (≠ S250), K224 (= K253), G255 (≠ A284), R357 (= R385)
4wxfA Crystal structure of l-serine hydroxymethyltransferase in complex with glycine (see paper)
29% identity, 86% coverage: 48:421/435 of query aligns to 20:396/410 of 4wxfA
- active site: T43 (≠ S71), L45 (= L73), G189 (= G217), A215 (= A244), T218 (≠ M247), R230 (≠ A259)
- binding n-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane]: S29 (≠ A57), Y49 (≠ P77), Y59 (≠ E87), S91 (= S119), G92 (= G120), S93 (≠ A121), H120 (= H148), S170 (= S198), D195 (= D223), A197 (= A225), H198 (= H226), H223 (≠ Y252), K224 (= K253), G255 (≠ A284), R357 (= R385)
1kl2A Crystal structure of serine hydroxymethyltransferase complexed with glycine and 5-formyl tetrahydrofolate (see paper)
31% identity, 79% coverage: 71:413/435 of query aligns to 45:385/405 of 1kl2A
- active site: Y51 (≠ P77), E53 (≠ L79), D197 (= D223), T223 (≠ S250), K226 (= K253), R232 (≠ A259)
- binding N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid: E53 (≠ L79), Y60 (= Y86), G121 (= G147), H122 (= H148), S172 (= S198), F251 (= F279), N341 (≠ I370)
- binding glycine: Y51 (≠ P77), Y61 (≠ E87), H200 (= H226), R357 (= R385)
- binding pyridoxal-5'-phosphate: S93 (= S119), G94 (= G120), A95 (= A121), H122 (= H148), S172 (= S198), D197 (= D223), A199 (= A225), H200 (= H226), T223 (≠ S250), H225 (≠ Y252), K226 (= K253)
Sites not aligning to the query:
Query Sequence
>GFF2427 PGA1_c24580 putative serine hydroxymethyltransferase
MPQAPQSWLPEASITRIEDITRATAGAGSDQLLDRIATLVEENRVIHEEDCFNLNPATNV
MNPKAEALLASGLGSRPSLGHPGDKYEMGLEAIEEIEVIAARLACEVFDAEFSEIRVPSG
ALANLYGFMATCRPGDTIIAPPASIGGHVTHHAAGCAGLYGLRSIEAPVLEDGYTVDLEA
LQQLAERERPKLITIGGSLNLFEHPVAGVRAIADQIGAKVMFDAAHQCGIIAGKAWADPL
AEGAHFMTMSTYKSLGGPAGGLIVSNDAEIAKALDSIAFPGMTANFDVAKSAALAVTLLD
WRDHGRAYASEMIAMAKSLAAALEAEGLPLFKTADGITMSHQFALCAAPYCGGQAASKLL
RKNGFLACGIGLPIPAVEGDMNGLRIGTPELVRWGMTSKDAAALAALIAAALRGEAVLDR
VSAWRRQFDRLHFVN
Or try a new SitesBLAST search
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