SitesBLAST
Comparing Dsui_2737 FitnessBrowser__PS:Dsui_2737 to proteins with known functional sites using BLASTp with E ≤ 0.001.
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Found 13 hits to proteins with known functional sites (download)
4lhdA Crystal structure of synechocystis sp. Pcc 6803 glycine decarboxylase (p-protein), holo form with pyridoxal-5'-phosphate and glycine, closed flexible loop (see paper)
57% identity, 98% coverage: 9:957/966 of query aligns to 6:949/952 of 4lhdA
- binding bicarbonate ion: S68 (≠ R67), Y70 (≠ H69), D141 (= D140), D480 (≠ H477), F838 (= F846), E863 (= E871), R866 (= R874), W923 (= W931), S948 (≠ A956)
- binding glycine: Y120 (= Y119), H609 (= H606), N633 (= N630), A666 (≠ E663), N803 (≠ K811), W845 (≠ F853), L903 (= L911), I904 (≠ A912), G906 (≠ E914), Q914 (≠ R922)
- binding phosphate ion: Q62 (≠ P61), L63 (= L62), P64 (= P63), W559 (= W556)
Sites not aligning to the query:
Q94B78 Glycine dehydrogenase (decarboxylating) 1, mitochondrial; Glycine cleavage system P protein 1; Glycine decarboxylase 1; Glycine decarboxylase P-protein 1; AtGLDP1; Glycine dehydrogenase (aminomethyl-transferring) 1; EC 1.4.4.2 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
54% identity, 99% coverage: 8:962/966 of query aligns to 69:1029/1037 of Q94B78
- C98 (≠ I37) modified: S-glutathionyl cysteine; transient
- C402 (= C337) modified: S-glutathionyl cysteine
- C463 (≠ L397) modified: S-glutathionyl cysteine
- C777 (≠ A712) modified: S-glutathionyl cysteine; transient
- C943 (≠ I876) modified: S-glutathionyl cysteine; transient
- C1022 (= C955) modified: S-glutathionyl cysteine; transient
6i34B Crystal structure of neanderthal glycine decarboxylase (p-protein)
54% identity, 98% coverage: 12:959/966 of query aligns to 7:954/954 of 6i34B
- binding pyridoxal-5'-phosphate: C332 (= C337), T333 (= T338), S507 (= S512), G568 (= G573), A569 (= A574), H601 (= H606), D677 (= D682), A679 (= A684), N701 (= N706), H703 (= H708), K704 (= K709)
6i33A Crystal structure of human glycine decarboxylase (p-protein)
54% identity, 98% coverage: 12:960/966 of query aligns to 9:950/950 of 6i33A
- binding bicarbonate ion: R413 (= R416), L414 (= L417)
- binding pyridoxal-5'-phosphate: C334 (= C337), T335 (= T338), S506 (= S512), G567 (= G573), A568 (= A574), H600 (= H606), D676 (= D682), A678 (= A684), N700 (= N706), H702 (= H708), K703 (= K709)
6i35A Crystal structure of human glycine decarboxylase (p-protein) bound with pyridoxyl-glycine-5'-monophosphate
54% identity, 98% coverage: 12:960/966 of query aligns to 9:953/953 of 6i35A
- binding n-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane]: Y113 (= Y116), C334 (= C337), T335 (= T338), S505 (= S512), C506 (= C513), G566 (= G573), A567 (= A574), H599 (= H606), T601 (= T608), D675 (= D682), A677 (= A684), N699 (= N706), H701 (= H708)
P15505 Glycine dehydrogenase (decarboxylating), mitochondrial; Glycine cleavage system P protein; Glycine decarboxylase; Glycine dehydrogenase (aminomethyl-transferring); EC 1.4.4.2 from Gallus gallus (Chicken) (see paper)
52% identity, 99% coverage: 12:964/966 of query aligns to 47:993/1004 of P15505
- K738 (= K709) modified: N6-(pyridoxal phosphate)lysine
6i33B Crystal structure of human glycine decarboxylase (p-protein)
52% identity, 98% coverage: 12:959/966 of query aligns to 7:925/925 of 6i33B
- binding pyridoxal-5'-phosphate: C332 (= C337), T333 (= T338), S507 (= S512), S567 (= S572), G568 (= G573), A569 (= A574), E572 (= E577), H593 (= H606), T595 (= T608), D651 (= D682), A653 (= A684), N675 (= N706), H677 (= H708), K678 (= K709)
1wyuB Crystal structure of glycine decarboxylase (p-protein) of the glycine cleavage system, in holo form (see paper)
41% identity, 41% coverage: 486:882/966 of query aligns to 46:436/473 of 1wyuB
1wyvA Crystal structure of glycine decarboxylase (p-protein) of the glycine cleavage system, in inhibitor-bound form (see paper)
36% identity, 40% coverage: 28:414/966 of query aligns to 9:399/437 of 1wyvA
1wyuA Crystal structure of glycine decarboxylase (p-protein) of the glycine cleavage system, in holo form (see paper)
36% identity, 40% coverage: 28:414/966 of query aligns to 9:399/437 of 1wyuA
1eqbA X-ray crystal structure at 2.7 angstroms resolution of ternary complex between the y65f mutant of e-coli serine hydroxymethyltransferase, glycine and 5-formyl tetrahydrofolate (see paper)
28% identity, 16% coverage: 546:704/966 of query aligns to 69:218/416 of 1eqbA
- active site: D199 (= D682)
- 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: L120 (≠ S604), G123 (= G607), G124 (vs. gap), H125 (vs. gap), L126 (vs. gap), S174 (≠ P655)
- binding glycine: H202 (≠ N685)
- binding pyridoxal-5'-phosphate: S96 (= S572), G97 (= G573), S98 (≠ A574), H125 (vs. gap), F173 (≠ Y654), S174 (≠ P655), D199 (= D682), H202 (≠ N685)
Sites not aligning to the query:
- active site: 54, 56, 225, 228, 234
- 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: 56, 63, 346, 354, 355, 356
- binding glycine: 34, 54, 64, 228, 362
- binding pyridoxal-5'-phosphate: 227, 228
1dfoB Crystal structure at 2.4 angstrom resolution of e. Coli serine hydroxymethyltransferase in complex with glycine and 5-formyl tetrahydrofolate (see paper)
28% identity, 16% coverage: 546:704/966 of query aligns to 70:219/417 of 1dfoB
- active site: D200 (= D682)
- 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: L121 (≠ S604), G125 (vs. gap), H126 (vs. gap), L127 (vs. gap), S175 (≠ P655)
- binding n-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane]: S97 (= S572), G98 (= G573), S99 (≠ A574), H126 (vs. gap), F174 (≠ Y654), S175 (≠ P655), D200 (= D682), A202 (= A684), H203 (≠ N685)
Sites not aligning to the query:
- active site: 55, 57, 226, 229, 235
- 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: 57, 64, 65, 245, 247, 347, 355, 356, 357
- binding n-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane]: 35, 55, 65, 229, 262, 363
P0A825 Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1 from Escherichia coli (strain K12) (see 8 papers)
28% identity, 16% coverage: 546:704/966 of query aligns to 70:219/417 of P0A825
- L85 (≠ V560) mutation to A: Alteration of the dimer-monomer equilibrium accompanied by minor changes in the catalytic properties and whitout any significant change of tertiary structure. In the monomeric state; when associated with A-276.
- P214 (≠ G699) mutation to A: No significant difference in catalytic efficiency and affinity compared to the wild-type.; mutation to G: No significant difference in catalytic efficiency and affinity compared to the wild-type.
- P216 (≠ D701) mutation to A: No significant difference in catalytic efficiency and affinity compared to the wild-type. Alteration in the folding rate.; mutation to G: Important decrease in affinity and catalytic efficiency. Severely compromised in folding into a catalytically competent enzyme.
- P218 (≠ S703) mutation to A: No significant difference in catalytic efficiency and affinity compared to the wild-type.; mutation to G: No significant difference in catalytic efficiency and affinity compared to the wild-type.
Sites not aligning to the query:
- 54 modified: N6-acetyllysine
- 55 Y→F: 50 and 15-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 4-fold decrease in the catalytic efficiency.
- 62 modified: N6-succinyllysine
- 65 Y→F: Decrease in catalytic activity.
- 228 Plays an important role in substrate specificity; binding ; mutation H->D,N: Utilize substrates and substrate analogs more effectively for a variety of alternate non-physiological reactions.
- 229 modified: N6-(pyridoxal phosphate)lysine
- 235 binding ; R→K: 1500- and 20-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 15-fold decrease in the catalytic efficiency.; R→L: 450- and 11-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 60-fold decrease in the catalytic efficiency.; R→Q: 900- and 17-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 30-fold decrease in the catalytic efficiency.
- 242 modified: N6-succinyllysine
- 250 modified: N6-acetyllysine; alternate; modified: N6-succinyllysine; alternate
- 258 P→A: Important decrease in affinity and catalytic efficiency. Reduced thermal stability.; P→G: Important decrease in affinity and catalytic efficiency.
- 264 P→A: Important decrease in affinity and catalytic efficiency.; P→G: Important decrease in affinity and catalytic efficiency.
- 276 L→A: Alteration of the dimer-monomer equilibrium accompanied by minor changes in the catalytic properties and whitout any significant change of tertiary structure. In the monomeric state; when associated with A-85.
- 277 modified: N6-succinyllysine
- 285 modified: N6-acetyllysine
- 293 modified: N6-succinyllysine
- 331 modified: N6-succinyllysine
- 346 modified: N6-succinyllysine
- 354 modified: N6-acetyllysine; alternate; modified: N6-succinyllysine; alternate
- 363 R→A: It does not bind serine and glycine and shows no activity with serine as the substrate.; R→K: Exhibits only 0.03% of the catalytic activity of the wild-type and a 15-fold reduction in affinity for glycine and serine.
- 372 R→A: No significant difference compared to the wild-type.; R→K: No significant difference compared to the wild-type.
- 375 modified: N6-acetyllysine
Query Sequence
>Dsui_2737 FitnessBrowser__PS:Dsui_2737
MSDTLPQSLSALEQKDEFIARHIGPCASEMSQMLAAIGAASLDQLVDQTVPAAIRFPADL
PLPAPRREHEALADLKALAGRNVVKKSLIGQGYHETLTPKVILRNVLENPGWYTAYTPYQ
AEIAQGRLEALLNYQQVIIDLTGLELANASLLDEATAAAEAMTMARRVSKSGSNRFFVDA
ACFPQTIDVVKTRAAYFGFELIFGPVEEAATVEVFGALLQYPNDKGEVQDLTATIAALKA
KGAVTAVACDLMALVLLKSPGAMGADMALGSSQRFGIPMGFGGPHAAFFACKDEHKRSVA
GRIIGVSVDARGNKALRMALQTREQHIRREKANSNICTSQVLLANMAGMYAVYHGPEGLK
TIARRIHRLAAILATGLAKAGIKQLNACYFDTLQLDLGAKALTVYQAAQNAGYNLRLIEG
GRLGIALNEKTTREDVATLLQLIAGVKVDIEALDAQVAAADPALPAELLRTDAILSHPVF
NTHHTEHEMLRYLKKLQNKDLALDHSMISLGSCTMKLNATSEMIPVTWPEFGDIHPFAPL
DQAQGYLEMIEQLAEWLKTVTGFDAVCMQPNSGAQGEYAGLVAIRRYQEANGQGQRDICL
IPKSAHGTNPATAQMAGLQVVVVDCDDNGNVDVADLKAKAEQHAAKLSCLMLTYPSTHGV
FEEAVKDICDIVHANGGQVYMDGANLNAQVGLTAPGFIGADVSHMNLHKTFAIPHGGGGP
GMGPIGLKAHLAPYMADHAVQATGPAERKHKGQGAVSAAPFGSASILPISWMYIAMLGGK
GVKTATQVAILNANYVAARLQEHYPVLYRGKNGRVAHECILDIRPIKAATGIAEIDIAKR
LMDYGFHAPTVSFPVAGTIMVEPTESESKAELDRFIDALIAIRNEIRKVEAGQWPADNNP
LKHAPHTQKDLADEVWSRPYSRQEACYPLAWVAENKFWPSVNRIDDVYGDRNLFCACAPV
EDYQHG
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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