2P02 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF HUMAN S-ADENOSYLMETHIONINE SYNTHETASE 2

Authors :   E. Papagrigoriou, N. Shafqat, A. Rojkova, F. H. Niessen, K. L. Kavanagh, F. Von Delft, F. Gorrec, E. Ugochukwu, C. H. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, U. Oppermann, Structural Genomics Consortium (Sgc)

Date :   28 Feb 07 (Deposition) - 13 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.21

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

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

Reference :   E. Papagrigoriou, N. Shafqat, A. Rojkova, F. H. Niessen, K. L. Kavanagh, F. Von Delft, F. Gorrec, E. Ugochukwu, C. H. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, U. Oppermann
Crystal Structure Of The Alpha Subunit Of Human S-Adenosylmethionine Synthetase 2
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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	ENST00000306434	1a	ENSE00001155028	chr2:85766288-85766501	214	METK2_HUMAN	1-31	31	1	A:38-53	16
1.3c	ENST00000306434	3c	ENSE00001765905	chr2:85768206-85768283	78	METK2_HUMAN	31-57	27	1	A:53-79	27
1.3e	ENST00000306434	3e	ENSE00001733360	chr2:85768378-85768500	123	METK2_HUMAN	57-98	42	1	A:79-120	42
1.3h	ENST00000306434	3h	ENSE00001135638	chr2:85768756-85768868	113	METK2_HUMAN	98-135	38	1	A:120-157	38
1.3j	ENST00000306434	3j	ENSE00001135633	chr2:85768952-85769095	144	METK2_HUMAN	136-183	48	1	A:158-205	48
1.3l	ENST00000306434	3l	ENSE00001135625	chr2:85769278-85769496	219	METK2_HUMAN	184-256	73	1	A:206-278	73
1.3n	ENST00000306434	3n	ENSE00001135613	chr2:85769688-85769870	183	METK2_HUMAN	257-317	61	1	A:279-339	61
1.4a	ENST00000306434	4a	ENSE00001135603	chr2:85770024-85770157	134	METK2_HUMAN	318-362	45	1	A:340-384	45
1.4f	ENST00000306434	4f	ENSE00001880464	chr2:85770793-85772403	1611	METK2_HUMAN	362-395	34	1	A:384-417	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:380
 aligned with METK2_HUMAN | P31153 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:380
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395
          METK2_HUMAN    16 GTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITSRAAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY 395
               SCOP domains d2p02a1 A:38-147 S-adenosylmethionine synthetase                                                              d2p02a2 A:148-273 S-adenosylmethionine synthetase                                                                             d2p02a3 A:274-417 S-adenosylmethionine synthetase                                                                                                SCOP domains
               CATH domains 2p02A01  2p02A02 A:47-149,A:275-311  [code=3.30.300.10, no name defined]                                        2p02A03                 2p02A01 A:38-46,A:174-274  [code=3.30.300.10, no name defined]                                       2p02A02 A:47-149,A:275-311           2p02A03 A:150-173,A:312-416  [code=3.30.300.10, no name defined]                                         - CATH domains
               Pfam domains S-AdoMet_synt_N-2p02A03 A:38-137                                                                    ------------S-AdoMet_synt_M-2p02A02 A:150-272                                                                                          -S-AdoMet_synt_C-2p02A01 A:274-411                                                                                                         ------ Pfam domains
         Sec.struct. author .eeeeeeeee...hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhh.eehhhhee....eeeeeee..hhhhhhhhh...hhhhh.....eeeeeeee.......hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh....eeee........hhhhh..ee...........................hhhhhhhhhhhhhhhhhhhh....eeeeeeee........eeeee.......hhhhhhhhhhhhh..hhhhhhhhhh....hhhhhh.........hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ADOMET_SYNT----------------------------------------------------------------------------------------------------------------------------------------ADOMET_SY------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a       -------------------------Exon 1.3e  PDB: A:79-120 UniProt: 57-98   -------------------------------------Exon 1.3j  PDB: A:158-205 UniProt: 136-183      Exon 1.3l  PDB: A:206-278 UniProt: 184-256                               Exon 1.3n  PDB: A:279-339 UniProt: 257-317                   Exon 1.4a  PDB: A:340-384 UniProt: 318-362   --------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.3c  PDB: A:53-79    ----------------------------------------Exon 1.3h  PDB: A:120-157             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4f  PDB: A:384-417          Transcript 1 (2)
                 2p02 A  38 GTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITSRAAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY 417
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417

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 (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (METK2_HUMAN | P31153)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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: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.
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.
	GO:0048269	methionine adenosyltransferase complex	A multimeric enzyme complex composed of variable numbers of catalytic alpha subunits, and noncatalytic beta subunits. The beta subunits are believed to have a regulatory function. The enzyme complex catalyzes the synthesis of S-adenosylmethionine (AdoMet), which is the major methyl group donor, participating in the methylation of proteins, DNA, RNA, phospholipids, and other small molecules.

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