SitesBLAST
Comparing WP_012674314.1 NCBI__GCF_000021545.1:WP_012674314.1 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)
8g3hA Structure of cobalamin-dependent methionine synthase (meth) in a resting state (see paper)
50% identity, 71% coverage: 3:835/1176 of query aligns to 6:829/841 of 8g3hA
- binding cobalamin: Q328 (= Q329), T330 (≠ P331), S331 (≠ P332), F675 (= F678), V685 (= V688), K693 (= K696), G720 (= G724), V722 (= V726), H723 (= H727), D724 (= D728), I725 (≠ V729), G726 (= G730), V730 (= V734), M767 (= M771), S768 (= S772), L770 (= L774), V772 (= V776), I795 (≠ L799), L796 (= L800), G797 (= G801), G798 (= G802), A799 (= A803), Y818 (= Y824), A819 (≠ C825), E820 (≠ R826), D821 (= D827)
P13009 Methionine synthase; 5-methyltetrahydrofolate--homocysteine methyltransferase; Methionine synthase, vitamin-B12-dependent; MS; EC 2.1.1.13 from Escherichia coli (strain K12) (see 5 papers)
31% identity, 100% coverage: 3:1176/1176 of query aligns to 8:1192/1227 of P13009
- C247 (= C221) binding Zn(2+)
- C310 (= C287) binding Zn(2+); mutation C->A,S: Loss of zinc binding. Loss of catalytic activity.
- C311 (= C288) binding Zn(2+); mutation C->A,S: Loss of zinc binding. Loss of catalytic activity.
- E694 (≠ N664) binding methylcob(III)alamin
- GDVHD 756:760 (= GDVHD 724:728) binding methylcob(III)alamin
- D757 (= D725) mutation to E: Decreases activity by about 70%.; mutation to N: Decreases activity by about 45%.
- H759 (= H727) binding axial binding residue; mutation to G: Loss of catalytic activity.
- S804 (= S772) binding methylcob(III)alamin
- T808 (≠ V776) binding methylcob(III)alamin
- S810 (= S778) mutation to A: Decreases activity by about 40%.
- A860 (= A828) binding methylcob(III)alamin
- D946 (≠ R908) binding S-adenosyl-L-methionine
- R1134 (= R1119) binding S-adenosyl-L-methionine
- YY 1189:1190 (≠ YF 1173:1174) binding S-adenosyl-L-methionine
Sites not aligning to the query:
- 1 modified: Initiator methionine, Removed
Q99707 Methionine synthase; MS; 5-methyltetrahydrofolate--homocysteine methyltransferase; Cobalamin-dependent methionine synthase; Vitamin-B12 dependent methionine synthase; EC 2.1.1.13 from Homo sapiens (Human) (see 6 papers)
34% identity, 71% coverage: 2:838/1176 of query aligns to 21:896/1265 of Q99707
- R61 (vs. gap) natural variant: R -> K
- C255 (≠ T216) to Y: in dbSNP:rs1140598
- GSR 382:384 (≠ GSK 344:346) binding (6S)-5,6,7,8-tetrahydrofolate
- D449 (= D408) binding (6S)-5,6,7,8-tetrahydrofolate
- N470 (= N429) binding (6S)-5,6,7,8-tetrahydrofolate
- D537 (= D496) binding (6S)-5,6,7,8-tetrahydrofolate
- N579 (= N538) binding (6S)-5,6,7,8-tetrahydrofolate
- R585 (vs. gap) binding (6S)-5,6,7,8-tetrahydrofolate
- R591 (= R548) binding (6S)-5,6,7,8-tetrahydrofolate
Sites not aligning to the query:
- 919 D → G: in dbSNP:rs1805087
- 963 D→E: Decreases binding to MTRR; when associated with N-1071.
- 1071 K→N: Decreases binding to MTRR; when associated with E-963.
8sseA Methionine synthase, c-terminal fragment, cobalamin and reactivation domains from thermus thermophilus hb8 (see paper)
41% identity, 47% coverage: 629:1176/1176 of query aligns to 1:506/507 of 8sseA
- binding cobalamin: H97 (= H727), G100 (= G730), V104 (= V734), S142 (= S772), L145 (= L775), V146 (= V776), I169 (≠ L799), G171 (= G801), G172 (= G802), A173 (= A803), H405 (= H1073), V409 (= V1077), S451 (= S1121), F452 (≠ P1122), G453 (= G1123), Y454 (= Y1124), Q463 (≠ N1133), L485 (≠ I1155), E488 (= E1158), A490 (≠ S1160), S492 (≠ D1162)
4cczA Crystal structure of human 5-methyltetrahydrofolate-homocysteine methyltransferase, the homocysteine and folate binding domains
32% identity, 51% coverage: 2:602/1176 of query aligns to 5:600/611 of 4cczA
- binding (6s)-5,6,7,8-tetrahydrofolate: E336 (= E338), G342 (= G344), R344 (≠ K346), N430 (= N429), M458 (≠ L457), D497 (= D496), G536 (= G535), S538 (= S537), N539 (= N538), F542 (= F541), R545 (vs. gap), R551 (= R548)
5vooA Methionine synthase folate-binding domain with methyltetrahydrofolate from thermus thermophilus hb8 (see paper)
53% identity, 24% coverage: 334:610/1176 of query aligns to 3:279/282 of 5vooA
- binding 5-methyl-5,6,7,8-tetrahydrofolic acid: E7 (= E338), R8 (= R339), G13 (= G344), S14 (= S345), K15 (= K346), D77 (= D408), N98 (= N429), D165 (= D496), G204 (= G535), N207 (= N538), F210 (= F541), R217 (= R548), I237 (= I568)
3bofA Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima complexed with zn2+ and homocysteine (see paper)
29% identity, 48% coverage: 2:571/1176 of query aligns to 6:539/560 of 3bofA
1q8jA Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima (cd2+, hcy, methyltetrahydrofolate complex) (see paper)
29% identity, 48% coverage: 2:571/1176 of query aligns to 6:539/559 of 1q8jA
- binding 5-methyl-5,6,7,8-tetrahydrofolic acid: E320 (= E338), D390 (= D408), N411 (= N429), D473 (= D496), G505 (= G535), N508 (= N538), F511 (= F541), R516 (= R548), I536 (= I568)
3k13C Structure of the pterin-binding domain metr of 5- methyltetrahydrofolate-homocysteine methyltransferase from bacteroides thetaiotaomicron
34% identity, 23% coverage: 336:606/1176 of query aligns to 7:281/287 of 3k13C
- binding n-[4-({[(6s)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-l-glutamic acid: E9 (= E338), G15 (= G344), R17 (≠ K346), N103 (= N429), D170 (= D496), G209 (= G535), S211 (= S537), N212 (= N538), R218 (vs. gap), R224 (= R548), I244 (= I568)
3ivaA Structure of the b12-dependent methionine synthase (meth) c-teminal half with adohcy bound (see paper)
41% identity, 17% coverage: 624:828/1176 of query aligns to 3:210/576 of 3ivaA
- active site: D107 (= D725), H109 (= H727), S160 (= S778)
- binding cobalamin: H109 (= H727), G112 (= G730), V116 (= V734), G152 (= G770), L153 (≠ M771), S154 (= S772), L156 (= L774), I157 (≠ L775), T158 (≠ V776), G183 (= G801), G184 (= G802), Q208 (≠ R826), N209 (≠ D827)
Sites not aligning to the query:
- binding cobalamin: 303, 443, 486, 488, 489, 495, 520, 521, 524, 527, 528
- binding s-adenosyl-l-homocysteine: 447, 484, 485, 489, 491, 539
3bulA E. Coli i690c/g743c meth c-terminal fragment (649-1227) (see paper)
41% identity, 17% coverage: 624:828/1176 of query aligns to 3:210/577 of 3bulA
- active site: D107 (= D725), H109 (= H727), S160 (= S778)
- binding cobalamin: H109 (= H727), V116 (= V734), G152 (= G770), L153 (≠ M771), S154 (= S772), L156 (= L774), I157 (≠ L775), T158 (≠ V776), G183 (= G801), G184 (= G802), Q208 (≠ R826), N209 (≠ D827), A210 (= A828)
Sites not aligning to the query:
- binding cobalamin: 213, 302, 443, 486, 487, 488, 489, 495, 498, 521, 524, 527, 528
1bmtA How a protein binds b12: a 3.O angstrom x-ray structure of the b12- binding domains of methionine synthase (see paper)
41% identity, 17% coverage: 624:828/1176 of query aligns to 3:210/246 of 1bmtA
- active site: D107 (= D725), H109 (= H727), S160 (= S778)
- binding co-methylcobalamin: E44 (≠ N664), M48 (≠ I668), M51 (= M671), G55 (= G675), L65 (= L685), V68 (= V688), D107 (= D725), V108 (= V726), H109 (= H727), D110 (= D728), I111 (≠ V729), I115 (≠ L733), G152 (= G770), L153 (≠ M771), S154 (= S772), L156 (= L774), I157 (≠ L775), T158 (≠ V776), G183 (= G801), G184 (= G802), A185 (= A803), V207 (≠ C825), N209 (≠ D827), A210 (= A828)
2i2xB Crystal structure of methanol:cobalamin methyltransferase complex mtabc from methanosarcina barkeri (see paper)
33% identity, 16% coverage: 634:818/1176 of query aligns to 43:227/258 of 2i2xB
- active site: D134 (= D725), H136 (= H727), T187 (≠ S778)
- binding 5-hydroxybenzimidazolylcob(iii)amide: G133 (= G724), D134 (= D725), V135 (= V726), H136 (= H727), D137 (= D728), I138 (≠ V729), G139 (= G730), V143 (= V734), T179 (≠ G770), T181 (≠ S772), L183 (= L774), M184 (≠ L775), T185 (≠ V776), A208 (≠ L799), G210 (= G801), G211 (= G802), G212 (≠ A803)
Sites not aligning to the query:
Q46EH4 Methanol--corrinoid protein; Methanol:corrinoid methyltransferase 1 subunit of 27 kDa; MT1 subunit 27 kDa from Methanosarcina barkeri (strain Fusaro / DSM 804) (see paper)
33% identity, 16% coverage: 634:818/1176 of query aligns to 43:227/258 of Q46EH4
- H129 (≠ G720) mutation to K: Does not affect cobalamin-binding.
- H136 (= H727) mutation H->G,K: Abolishes cobalamin-binding.
Sites not aligning to the query:
- 256:258 HKH→KKK: Does not affect cobalamin-binding.
2yckX Methyltransferase bound with tetrahydrofolate (see paper)
32% identity, 20% coverage: 334:569/1176 of query aligns to 12:238/272 of 2yckX
- binding (6s)-5,6,7,8-tetrahydrofolate: M21 (≠ T343), F22 (≠ S345), D85 (= D408), N106 (= N429), D170 (= D496), G206 (= G535), N209 (= N538), Q212 (≠ F541), K213 (≠ G542), R217 (= R548), I237 (= I568)
2ycjA Methyltransferase bound with methyltetrahydrofolate (see paper)
32% identity, 20% coverage: 334:569/1176 of query aligns to 11:237/271 of 2ycjA
- binding 5-methyl-5,6,7,8-tetrahydrofolic acid: M20 (≠ T343), F21 (≠ S345), D84 (= D408), N105 (= N429), D169 (= D496), G205 (= G535), N208 (= N538), Q211 (≠ F541), R216 (= R548), I236 (= I568)
2yciX Methyltransferase native (see paper)
32% identity, 20% coverage: 334:569/1176 of query aligns to 11:237/271 of 2yciX
1y80A Structure of a corrinoid (factor iiim)-binding protein from moorella thermoacetica
43% identity, 8% coverage: 717:812/1176 of query aligns to 7:104/125 of 1y80A
- active site: D15 (= D725), H17 (= H727), T68 (≠ S778)
- binding co-5-methoxybenzimidazolylcobamide: D15 (= D725), L16 (≠ V726), H17 (= H727), D18 (= D728), I19 (≠ V729), G20 (= G730), V24 (= V734), G60 (= G770), M61 (= M771), S62 (= S772), L64 (= L774), L65 (= L775), T66 (≠ V776), I91 (≠ L799), G93 (= G801), G94 (= G802), A95 (= A803)
Sites not aligning to the query:
4djfA Crystal structure of folate-bound corrinoid iron-sulfur protein (cfesp) in complex with its methyltransferase (metr), co-crystallized with folate and ti(iii) citrate reductant (see paper)
31% identity, 20% coverage: 334:570/1176 of query aligns to 2:229/262 of 4djfA
- binding 5-methyl-5,6,7,8-tetrahydrofolic acid: E6 (= E338), M11 (≠ T343), F12 (≠ G344), D75 (= D408), N96 (= N429), D160 (= D496), S198 (= S537), N199 (= N538), R207 (= R548)
- binding calcium ion: G222 (= G563), D224 (≠ T565)
- binding co-methylcobalamin: V168 (≠ S504), Q202 (≠ L543), N203 (≠ D544)
4djeA Crystal structure of folate-bound corrinoid iron-sulfur protein (cfesp) in complex with its methyltransferase (metr), co-crystallized with folate (see paper)
31% identity, 20% coverage: 334:570/1176 of query aligns to 2:229/262 of 4djeA
- binding cobalamin: V168 (≠ S504), N203 (≠ D544)
- binding 5-methyl-5,6,7,8-tetrahydrofolic acid: E6 (= E338), M11 (≠ T343), F12 (≠ G344), D75 (= D408), N96 (= N429), D160 (= D496), G196 (= G535), S198 (= S537), N199 (= N538), R207 (= R548)
- binding calcium ion: G222 (= G563), D224 (≠ T565)
Query Sequence
>WP_012674314.1 NCBI__GCF_000021545.1:WP_012674314.1
MDLRSLIKERVLVIDGAMGTMIQSTIIPMSAWDGKVGCNEILNITAPQIIQNIHEKYLQA
GADIIKTNTFGALPWVLEEYGIPDKAYELAKAGALLVKQLCDKYSTAEKPRFVAGSLGPG
TKLPSLGHIDYDTMYEGYKVAAYGLIDGGVDVFLVETCQDPLQIKVALHALNDASKERRK
DIPIMVSATIELTGTMLIGTDAQTLAAIMEPFDILTLGFNCGTGPDQVEQHLRKLSQVWK
GYISVHANAGLPENRGGQTYYPMNAEEFAEKESKFLDIDGVAIVGGCCGTTPSHIKALYE
KVKGKKPKKPVGKQPKSLASLFMTQPLKQDPPPFLVGERTNATGSKQFRELLLKEDYDGI
LAIAQDQVKSGSHALDVSVNYAGRDEIKDMKEVIRRFNEKIPIPLMVDSTQPKAIEAGLK
HIGGKPIINSANLEDSEEKFDKICQLAKRFGTSLVLLAIDEQGMAKTKERKLEVAERMYE
RATKVHGLDPEDLVFDLLTFTVGSGDQEYRDAAVQTIEAIRELRKRHPEVGAVLGISNVS
FGLDMHARKYLNSVFLHHCVEAGLTMAIVNPKHLIPFHKISEEDRKVCENLLFNVWENGK
DPLFEFIHYFSKKKESILSEESKDFKNLPIEEKIKKLLIDGEKEKLIKAVEEARHKIPPE
KIINEILIDAMKIVGDLFGEGKMQLPFVLQSAESMKAAVDYLNQFLPKTTKKKKTTLVLG
TVKGDVHDVGKNLVDIILTNNGFNVVNLGIKVELEQFLKAAEEHKADAIGMSGLLVKSTL
EMKNNLEEMQKRGIKIPVLLGGAALNKKFVDEYCRPVYDGPIFYCRDAFDGIEAMTRIEK
GIFDTDLGYKEEEETQVKIEEKLEIPPLKDIKMPSMDVVVPTPPFWGRKVWIHPDSPEYE
EIRELAFRWINKGALFKRAWGYTRGDKSREEYEKLKKEEILPNFERLKKLLIENDLFNPI
IIYGYYPCRSDFPIRLKNNDNRESSLLIFPPSEGWKSEEDVNREPLENILDRVYKKIDFP
RSSKPPYRSLSDYFHHDRHDVVAFTVVSAGKKLSEYENELFKQGKYKDYHLIHGLGVELA
EALAEIVHKKIRIELGIAKAEGESLYDVNWQIRNYQGARYSPGYPACPDLAINDIIFDIL
KPQEYGITLTENHLIVPEQSTDAIVVYHPEATYFSV
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