2OBV - JenaLib

Title :   CRYSTAL STRUCTURE OF THE HUMAN S-ADENOSYLMETHIONINE SYNTHETASE 1 IN COMPLEX WITH THE PRODUCT

Authors :   E. S. Pilka, N. Shafqat, K. L. Kavanagh, C. Cooper, V. Hozjan, A. Turnbul Delft, C. H. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, U. Oppe Structural Genomics Consortium (Sgc)

Date :   20 Dec 06 (Deposition) - 02 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (4x)

Keywords :   Synthetase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. S. Pilka, N. Shafqat, K. L. Kavanagh, C. Cooper, V. Hozjan, A. Turnbull, F. Von Delft, C. H. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, U. Oppermann, Structural Genomics Consortium (Sgc
Crystal Structure Of The Human S-Adenosylmethionine Synthetase 1 In Complex With The Product.
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (13, 13)

Asymmetric Unit (13, 13)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_031242	S	38	N	METK1_HUMAN	Disease (MATD)	---	A	S	38	N
02	UniProt	VAR_006935	A	55	D	METK1_HUMAN	Disease (MATD)	118204002	A	A	55	D
03	UniProt	VAR_028944	Q	119	H	METK1_HUMAN	Polymorphism	1143693	A	Q	119	H
04	UniProt	VAR_006936	R	199	C	METK1_HUMAN	Disease (MATD)	773267230	A	R	199	C
05	UniProt	VAR_031243	R	264	C	METK1_HUMAN	Disease (MATD)	118204005	A	R	264	C
06	UniProt	VAR_006937	R	264	H	METK1_HUMAN	Disease (MATD)	72558181	A	R	264	H
07	UniProt	VAR_006938	L	305	P	METK1_HUMAN	Disease (MATD)	118204004	A	L	305	P
08	UniProt	VAR_006939	I	322	M	METK1_HUMAN	Disease (MATD)	118204001	A	I	322	M
09	UniProt	VAR_031244	G	336	R	METK1_HUMAN	Disease (MATD)	118204006	A	G	336	R
10	UniProt	VAR_031245	E	344	A	METK1_HUMAN	Disease (MATD)	---	A	E	344	A
11	UniProt	VAR_006940	R	356	Q	METK1_HUMAN	Disease (MATD)	138742870	A	R	356	Q
12	UniProt	VAR_006941	P	357	L	METK1_HUMAN	Disease (MATD)	118204003	A	P	357	L
13	UniProt	VAR_006942	G	378	S	METK1_HUMAN	Disease (MATD)	---	A	G	378	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (13, 26)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_031242	S	38	N	METK1_HUMAN	Disease (MATD)	---	A	S	38	N
02	UniProt	VAR_006935	A	55	D	METK1_HUMAN	Disease (MATD)	118204002	A	A	55	D
03	UniProt	VAR_028944	Q	119	H	METK1_HUMAN	Polymorphism	1143693	A	Q	119	H
04	UniProt	VAR_006936	R	199	C	METK1_HUMAN	Disease (MATD)	773267230	A	R	199	C
05	UniProt	VAR_031243	R	264	C	METK1_HUMAN	Disease (MATD)	118204005	A	R	264	C
06	UniProt	VAR_006937	R	264	H	METK1_HUMAN	Disease (MATD)	72558181	A	R	264	H
07	UniProt	VAR_006938	L	305	P	METK1_HUMAN	Disease (MATD)	118204004	A	L	305	P
08	UniProt	VAR_006939	I	322	M	METK1_HUMAN	Disease (MATD)	118204001	A	I	322	M
09	UniProt	VAR_031244	G	336	R	METK1_HUMAN	Disease (MATD)	118204006	A	G	336	R
10	UniProt	VAR_031245	E	344	A	METK1_HUMAN	Disease (MATD)	---	A	E	344	A
11	UniProt	VAR_006940	R	356	Q	METK1_HUMAN	Disease (MATD)	138742870	A	R	356	Q
12	UniProt	VAR_006941	P	357	L	METK1_HUMAN	Disease (MATD)	118204003	A	P	357	L
13	UniProt	VAR_006942	G	378	S	METK1_HUMAN	Disease (MATD)	---	A	G	378	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (13, 52)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_031242	S	38	N	METK1_HUMAN	Disease (MATD)	---	A	S	38	N
02	UniProt	VAR_006935	A	55	D	METK1_HUMAN	Disease (MATD)	118204002	A	A	55	D
03	UniProt	VAR_028944	Q	119	H	METK1_HUMAN	Polymorphism	1143693	A	Q	119	H
04	UniProt	VAR_006936	R	199	C	METK1_HUMAN	Disease (MATD)	773267230	A	R	199	C
05	UniProt	VAR_031243	R	264	C	METK1_HUMAN	Disease (MATD)	118204005	A	R	264	C
06	UniProt	VAR_006937	R	264	H	METK1_HUMAN	Disease (MATD)	72558181	A	R	264	H
07	UniProt	VAR_006938	L	305	P	METK1_HUMAN	Disease (MATD)	118204004	A	L	305	P
08	UniProt	VAR_006939	I	322	M	METK1_HUMAN	Disease (MATD)	118204001	A	I	322	M
09	UniProt	VAR_031244	G	336	R	METK1_HUMAN	Disease (MATD)	118204006	A	G	336	R
10	UniProt	VAR_031245	E	344	A	METK1_HUMAN	Disease (MATD)	---	A	E	344	A
11	UniProt	VAR_006940	R	356	Q	METK1_HUMAN	Disease (MATD)	138742870	A	R	356	Q
12	UniProt	VAR_006941	P	357	L	METK1_HUMAN	Disease (MATD)	118204003	A	P	357	L
13	UniProt	VAR_006942	G	378	S	METK1_HUMAN	Disease (MATD)	---	A	G	378	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (2, 2)

Exons (9, 9)

Asymmetric Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000372213	1a	ENSE00001910847	chr10:82049440-82049089	352	METK1_HUMAN	1-31	31	1	A:-3-31	20
1.2	ENST00000372213	2	ENSE00000998389	chr10:82045345-82045268	78	METK1_HUMAN	31-57	27	1	A:31-57	27
1.3	ENST00000372213	3	ENSE00000998397	chr10:82043794-82043672	123	METK1_HUMAN	57-98	42	1	A:57-98	42
1.4	ENST00000372213	4	ENSE00000998396	chr10:82040548-82040436	113	METK1_HUMAN	98-135	38	1	A:98-135	38
1.5	ENST00000372213	5	ENSE00000998391	chr10:82040072-82039929	144	METK1_HUMAN	136-183	48	1	A:136-183	48
1.6b	ENST00000372213	6b	ENSE00002176570	chr10:82036350-82036132	219	METK1_HUMAN	184-256	73	1	A:184-256	73
1.7b	ENST00000372213	7b	ENSE00001598810	chr10:82034955-82034773	183	METK1_HUMAN	257-317	61	1	A:257-317	61
1.8	ENST00000372213	8	ENSE00001677786	chr10:82034409-82034276	134	METK1_HUMAN	318-362	45	1	A:318-362	45
1.9c	ENST00000372213	9c	ENSE00001836450	chr10:82033639-82031576	2064	METK1_HUMAN	362-395	34	1	A:362-395	34

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:384
 aligned with METK1_HUMAN | Q00266 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:384
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391    
          METK1_HUMAN    12 SLSEGVFMFTSESVGEGHPDKICDQISDAVLDAHLKQDPNAKVACETVCKTGMVLLCGEITSMAMVDYQRVVRDTIKHIGYDDSAKGFDFKTCNVLVALEQQSPDIAQCVHLDRNEEDVGAGDQGLMFGYATDETEECMPLTIILAHKLNARMADLRRSGLLPWLRPDSKTQVTVQYMQDNGAVIPVRIHTIVISVQHNEDITLEEMRRALKEQVIRAVVPAKYLDEDTVYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRRVLVQVSYAIGVAEPLSISIFTYGTSQKTERELLDVVHKNFDLRPGVIVRDLDLKKPIYQKTACYGHFGRSEFPWEVPRKLVF 395
               SCOP domains d2obva1 A:-3-125 automated matches                                                                                d2obva2 A:126-251 automated matches                                                                                           d2obva3 A:252-395 automated matches                                                                                                              SCOP domains
               CATH domains 2obvA01      2obvA02 A:25-128,A:253-289  [code=3.30.300.10, no name defined]                                         2obvA03                2obvA01 A:-3-24,A:152-252  [code=3.30.300.10, no name defined]                                       2obvA02 A:25-128,A:253-289           2obvA03 A:129-151,A:290-394  [code=3.30.300.10, no name defined]                                         - CATH domains
               Pfam domains ----S-AdoMet_synt_N-2obvA03 A:16-115                                                                    ------------S-AdoMet_synt_M-2obvA02 A:128-250                                                                                          -S-AdoMet_synt_C-2obvA01 A:252-389                                                                                                         ------ Pfam domains
         Sec.struct. author hhhhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhh.eehhhhee....eeeeeee..hhhhhhhhh...hhhhh.....eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh....eeee........hhhhh..ee...........................hhhhhhhhhhhhhhhhhhhh....eeeeeeee........eeeee.......hhhhhhhhhhhhh..hhhhhhhhh.....hhhhhh.........hhhhh...... Sec.struct. author
             SAPs(SNPs) (1) --------------------------N----------------D---------------------------------------------------------------H-------------------------------------------------------------------------------C----------------------------------------------------------------C----------------------------------------P----------------M-------------R-------A-----------QL--------------------S----------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------ADOMET_SYNT----------------------------------------------------------------------------------------------------------------------------------------ADOMET_SY------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a           -------------------------Exon 1.3  PDB: A:57-98 UniProt: 57-98     -------------------------------------Exon 1.5  PDB: A:136-183 UniProt: 136-183       Exon 1.6b  PDB: A:184-256 UniProt: 184-256                               Exon 1.7b  PDB: A:257-317 UniProt: 257-317                   Exon 1.8  PDB: A:318-362 UniProt: 318-362    --------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: A:31-57     ----------------------------------------Exon 1.4  PDB: A:98-135               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9c  PDB: A:362-395          Transcript 1 (2)
                 2obv A  -3 FQSMGVFMFTSESVGEGHPDKICDQISDAVLDAHLKQDPNAKVACETVCKTGMVLLCGEITSMAMVDYQRVVRDTIKHIGYDDSAKGFDFKTCNVLVALEQQSPDIAQCVHLDRNEEDVGAGDQGLMFGYATDETEECMPLTIILAHKLNARMADLRRSGLLPWLRPDSKTQVTVQYMQDNGAVIPVRIHTIVISVQHNEDITLEEMRRALKEQVIRAVVPAKYLDEDTVYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRRVLVQVSYAIGVAEPLSISIFTYGTSQKTERELLDVVHKNFDLRPGVIVRDLDLKKPIYQKTACYGHFGRSEFPWEVPRKLVF 395
                               ||   21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391    
                               0|                                                                                                                                                                                                                                                                                                                                                                                           
                               16

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (3, 3)

Gene Ontology (13, 13)

Asymmetric Unit(hide GO term definitions)

Chain A (METK1_HUMAN | Q00266)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004478	methionine adenosyltransferase activity	Catalysis of the reaction: ATP + L-methionine + H2O = phosphate + diphosphate + S-adenosyl-L-methionine.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0098601	selenomethionine adenosyltransferase activity	Catalysis of the reaction: ATP + L-Selenomethionine + H2O => Orthophosphate + Diphosphate + Se-Adenosylselenomethionine.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006556	S-adenosylmethionine biosynthetic process	The chemical reactions and pathways resulting in the formation of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0001887	selenium compound metabolic process	The chemical reactions and pathways involving compounds that contain selenium, such as selenocysteine.
	GO:0000096	sulfur amino acid metabolic process	The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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