1R74 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN GLYCINE N-METHYLTRANSFERASE

Authors :   S. Pakhomova, Z. Luka, C. Wagner, M. E. Newcomer

Date :   17 Oct 03 (Deposition) - 21 Sep 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Glycine N-Methyltransferase, Human, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Pakhomova, Z. Luka, S. Grohmann, C. Wagner, M. E. Newcomer
Glycine N-Methyltransferases: A Comparison Of The Crystal Structures And Kinetic Properties Of Recombinant Human, Mouse And Rat Enzymes.
Proteins V. 57 331 2004
PubMed-ID: 15340920 | Reference-DOI: 10.1002/PROT.20209

Molecule 1 - GLYCINE N-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGE3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET17B
	Expression System Vector Type	:	PLASMID
	Gene	:	GNMT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	BME	4	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CIT	2	Ligand/Ion	CITRIC ACID

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	BME	8	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CIT	4	Ligand/Ion	CITRIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:54 , GLY A:186 , CYS A:187 , VAL A:204 , THR A:206 , ASN A:212	BINDING SITE FOR RESIDUE BME A 1187
2	AC2	SOFTWARE	TYR A:33 , GLY A:139 , ASN A:140 , HIS A:144 , ASN A:193 , TYR A:244 , TYR A:285 , GLU B:15	BINDING SITE FOR RESIDUE CIT A 1001
3	AC3	SOFTWARE	ARG B:53 , GLN B:54 , GLY B:56 , GLY B:186 , CYS B:187 , VAL B:204 , THR B:206 , ASN B:212	BINDING SITE FOR RESIDUE BME B 2187
4	AC4	SOFTWARE	GLN B:257 , CYS B:264 , GLN B:265 , HIS B:266	BINDING SITE FOR RESIDUE BME B 2264
5	AC5	SOFTWARE	LYS B:192 , CYS B:284	BINDING SITE FOR RESIDUE BME B 2284
6	AC6	SOFTWARE	TYR B:33 , GLY B:139 , ASN B:140 , HIS B:144 , ASN B:193 , TYR B:222 , TYR B:244 , TYR B:285 , HOH B:2286 , HOH B:2320	BINDING SITE FOR RESIDUE CIT B 2001

(no "SS Bond" information available for 1R74)

(no "Cis Peptide Bond" information available for 1R74)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012766	L	50	P	GNMT_HUMAN	Disease (GNMT deficiency)	121907888	A/B	L	49	P
2	UniProt	VAR_019840	N	141	S	GNMT_HUMAN	Disease (GNMT deficiency)	864321678	A/B	N	140	S
3	UniProt	VAR_012767	H	177	N	GNMT_HUMAN	Disease (GNMT deficiency)	121907889	A/B	H	176	N

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

Biological Unit 1 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012766	L	50	P	GNMT_HUMAN	Disease (GNMT deficiency)	121907888	A/B	L	49	P
2	UniProt	VAR_019840	N	141	S	GNMT_HUMAN	Disease (GNMT deficiency)	864321678	A/B	N	140	S
3	UniProt	VAR_012767	H	177	N	GNMT_HUMAN	Disease (GNMT deficiency)	121907889	A/B	H	176	N

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

(no "PROSITE Motif" information available for 1R74)

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000372808	1	ENSE00001458743	chr6:42928496-42928711	216	GNMT_HUMAN	1-69	69	2	A:5-68 B:5-68	64 64
1.2	ENST00000372808	2	ENSE00000850009	chr6:42929950-42930077	128	GNMT_HUMAN	69-112	44	2	A:68-111 B:68-111	44 44
1.3	ENST00000372808	3	ENSE00000850010	chr6:42930500-42930616	117	GNMT_HUMAN	112-151	40	2	A:111-150 (gaps) B:111-150	40 40
1.4	ENST00000372808	4	ENSE00000850011	chr6:42930810-42930952	143	GNMT_HUMAN	151-198	48	2	A:150-197 B:150-197	48 48
1.5	ENST00000372808	5	ENSE00000850012	chr6:42931066-42931187	122	GNMT_HUMAN	199-239	41	2	A:198-238 (gaps) B:198-238 (gaps)	41 41
1.6	ENST00000372808	6	ENSE00001458709	chr6:42931273-42931618	346	GNMT_HUMAN	239-295	57	2	A:238-293 B:238-293	56 56

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:275
 aligned with GNMT_HUMAN | Q14749 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:289
                                    15        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         
           GNMT_HUMAN     6 YRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCQRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRHEPAFDKWVIEEANWMTLDKDVPQSAEGGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRAGGLLVIDHRNYDHILSTGCAPPGKNIYYKSDLTKDVTTSVLIVNNKAHMVTLDYTVQVPGAGQDGSPGLSKFRLSYYPHCLASFTELLQAAFGGKCQHSVLGDFKPYKPGQTYIPCYFIHVLKRT 294
               SCOP domains d1r74a_ A: Glycine N-methyltransferase                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -----------------1r74A01         1r74A02 A:38-177,A:245-293 Vaccinia Virus protein VP39                                                                                      1r74A01 A:22-37,A:178-244                                          1r74A02 A:38-177,A:245-293                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................h.hhhh..............hhhhhhhhh........eee....hhhhhhh.hhh...eeee....hhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.---...eeeeee...hhhhh........hhhhhh.hhhh.eeeeeeeeeeeehhhhhhhhh................eeeeeeeee..eeeeeeeeee.-----------.....eeee...hhhhhhhhhhhhh......eeee..ee..........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------P------------------------------------------------------------------------------------------S-----------------------------------N--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:5-68 UniProt: 1-69 [INCOMPLETE]                ------------------------------------------Exon 1.3  PDB: A:111-150 (gaps)         -----------------------------------------------Exon 1.5  PDB: A:198-238 (gaps)          ------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.2  PDB: A:68-111 UniProt: 69-112     --------------------------------------Exon 1.4  PDB: A:150-197 UniProt: 151-198       ----------------------------------------Exon 1.6  PDB: A:238-293 UniProt: 239-295 [INCOMPLETE]   Transcript 1 (2)
                 1r74 A   5 YRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCQRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRHEPAFDKWVIEEANWMTLDKDVP---EGGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRAGGLLVIDHRNYDHILSTGCAPPGKNIYYKSDLTKDVTTSVLIVNNKAHMVTLDYTV-----------GLSKFRLSYYPHCLASFTELLQAAFGGKCQHSVLGDFKPYKPGQTYIPCYFIHVLKRT 293
                                    14        24        34        44        54        64        74        84        94       104       114       124|   |  134       144       154       164       174       184       194       204       214       224         - |     244       254       264       274       284         
                                                                                                                                                  125 129                                                                                            224         236

Chain B from PDB  Type:PROTEIN  Length:279
 aligned with GNMT_HUMAN | Q14749 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:289
                                    15        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         
           GNMT_HUMAN     6 YRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCQRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRHEPAFDKWVIEEANWMTLDKDVPQSAEGGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRAGGLLVIDHRNYDHILSTGCAPPGKNIYYKSDLTKDVTTSVLIVNNKAHMVTLDYTVQVPGAGQDGSPGLSKFRLSYYPHCLASFTELLQAAFGGKCQHSVLGDFKPYKPGQTYIPCYFIHVLKRT 294
               SCOP domains d1r74b_ B: Glycine N-methyltransferase                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -----------------1r74B01         1r74B02 B:38-177,B:245-293 Vaccinia Virus protein VP39                                                                                      1r74B01 B:22-37,B:178-244                                          1r74B02 B:38-177,B:245-293                        CATH domains
           Pfam domains (1) ---------------------------------------------------Methyltransf_18-1r74B01 B:56-177                                                                                          -------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------Methyltransf_18-1r74B02 B:56-177                                                                                          -------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ........................hhhhhh......hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.......eeeeee...hhhhh......hhhhhhhh.hhhh.eeeeeeeeeeeehhhhhhhhh...............eeeeeeeeee..eeeeeeeeeee.----------..eeeeeee...hhhhhhhhhhhhh...eeeeeee..ee..........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------P------------------------------------------------------------------------------------------S-----------------------------------N--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:5-68 UniProt: 1-69 [INCOMPLETE]                ------------------------------------------Exon 1.3  PDB: B:111-150                -----------------------------------------------Exon 1.5  PDB: B:198-238 (gaps)          ------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.2  PDB: B:68-111 UniProt: 69-112     --------------------------------------Exon 1.4  PDB: B:150-197 UniProt: 151-198       ----------------------------------------Exon 1.6  PDB: B:238-293 UniProt: 239-295 [INCOMPLETE]   Transcript 1 (2)
                 1r74 B   5 YRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCQRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRHEPAFDKWVIEEANWMTLDKDVPQSAEGGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRAGGLLVIDHRNYDHILSTGCAPPGKNIYYKSDLTKDVTTSVLIVNNKAHMVTLDYTVQ----------GLSKFRLSYYPHCLASFTELLQAAFGGKCQHSVLGDFKPYKPGQTYIPCYFIHVLKRT 293
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224|        - |     244       254       264       274       284         
                                                                                                                                                                                                                                                      225        236

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: Glycine N-methyltransferase (16)

Protein domain: Glycine N-methyltransferase (16)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d1r74a_	A:
1b	d1r74b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Glycine N-methyltransferase; chain A, domain 1 (14)

Homologous Superfamily: Glycine N-methyltransferase, chain A, domain 1 (14)

Human (Homo sapiens) (2)

1a	1r74B01	B:22-37,B:178-244
1b	1r74A01	A:22-37,A:178-244

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Human (Homo sapiens) (49)

2a	1r74B02	B:38-177,B:245-293
2b	1r74A02	A:38-177,A:245-293

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Methyltransf_18 (13)

Homo sapiens (Human) (1)

1a	Methyltransf_18-1r74B01	B:56-177
1b	Methyltransf_18-1r74B02	B:56-177

Asymmetric Unit(hide GO term definitions)

Chain A,B (GNMT_HUMAN | Q14749)

molecular function
	GO:0005542	folic acid binding	Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
	GO:0017174	glycine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine.
	GO:0016594	glycine binding	Interacting selectively and non-covalently with glycine, aminoethanoic acid.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0046500	S-adenosylmethionine metabolic process	The chemical reactions and pathways involving S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0005977	glycogen metabolic process	The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
	GO:0046487	glyoxylate metabolic process	The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
	GO:0006555	methionine metabolic process	The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	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:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0006111	regulation of gluconeogenesis	Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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	1r74
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(no "Related Entries Specified in the PDB File" available for 1R74)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

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Exons (6, 12)

Sequences/Alignments

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