2A14 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF HUMAN INDOLETHYLAMINE N-METHYLTRANSFERASE WITH SAH

Authors :   A. Dong, H. Wu, H. Zeng, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)

Date :   17 Jun 05 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

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

Reference :   H. Wu, A. Dong, H. Zeng, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
The Crystal Structure Of Human Indolethylamine N-Methyltransferase In Complex With Sah.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - INDOLETHYLAMINE N-METHYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.1.1.49
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:200 , GLU A:217 , LYS A:218 , ASN A:250 , ARG A:258 , HOH A:4093 , HOH A:4234	BINDING SITE FOR RESIDUE SO4 A 2003
2	AC2	SOFTWARE	TYR A:20 , TYR A:25 , GLY A:63 , SER A:64 , GLY A:65 , THR A:67 , TYR A:69 , ASP A:85 , PHE A:86 , THR A:87 , ASN A:90 , CYS A:141 , ASP A:142 , VAL A:143 , HIS A:144 , LEU A:163 , LEU A:164 , ALA A:165 , ALA A:169 , HOH A:4050 , HOH A:4064	BINDING SITE FOR RESIDUE SAH A 4001

(no "SS Bond" information available for 2A14)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:150	-	Pro A:151

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036991	D	28	N	INMT_HUMAN	Polymorphism	4723010	A	D	28	N
2	UniProt	VAR_011616	M	205	V	INMT_HUMAN	Polymorphism	2302339	A	M	205	V
3	UniProt	VAR_061373	V	214	M	INMT_HUMAN	Polymorphism	56800285	A	V	214	M
4	UniProt	VAR_011617	E	219	G	INMT_HUMAN	Polymorphism	2302340	A	G	219	G
5	UniProt	VAR_036992	N	246	S	INMT_HUMAN	Polymorphism	6970210	A	N	246	S
6	UniProt	VAR_036993	F	254	C	INMT_HUMAN	Polymorphism	4720015	A	C	254	C
7	UniProt	VAR_036994	R	258	H	INMT_HUMAN	Polymorphism	6970605	A	R	258	H

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_NNMT_PNMT_TEMT	PS51681	SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.	INMT_HUMAN	8-262	1	A:8-261
2	NNMT_PNMT_TEMT	PS01100	NNMT/PNMT/TEMT family of methyltransferases signature.	INMT_HUMAN	59-75	1	A:59-75

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.4a	ENST00000013222	4a	ENSE00000832209	chr7:30791751-30791920	170	INMT_HUMAN	1-52	52	1	A:5-52	48
1.5a	ENST00000013222	5a	ENSE00002156450	chr7:30793347-30793554	208	INMT_HUMAN	52-121	70	1	A:52-121	70
1.6c	ENST00000013222	6c	ENSE00001310197	chr7:30795038-30797218	2181	INMT_HUMAN	121-263	143	1	A:121-261	141

Asymmetric/Biological 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:257
 aligned with INMT_HUMAN | O95050 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:257
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
           INMT_HUMAN     5 FTGGDEYQKHFLPRDYLATYYSFDGSPSPEAEMLKFNLECLHKTFGPGGLQGDTLIDIGSGPTIYQVLAACDSFQDITLSDFTDRNREELEKWLKKEPGAYDWTPAVKFACELEGNSGRWEEKEEKLRAAVKRVLKCDVHLGNPLAPAVLPLADCVLTLLAMECACCSLDAYRAALCNLASLLKPGGHLVTTVTLRLPSYMVGKREFSCVALEKEEVEQAVLDAGFDIEQLLHSPQSYSVTNAANNGVCFIVARKKP 261
               SCOP domains d2a14a1 A:5-261 Indolethylamine N-methyltransferase, INMT                                                                                                                                                                                                         SCOP domains
               CATH domains 2a14A00 A:5-261 Vaccinia Virus protein VP39                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhh.eeeeeeee.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeee....eeee..eeee....hhhhhhhhhhhh.eeeeeeeee.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------N--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V--------M----G--------------------------S-------C---H--- SAPs(SNPs)
                PROSITE (1) ---SAM_MT_NNMT_PNMT_TEMT  PDB: A:8-261 UniProt: 8-262                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) ------------------------------------------------------NNMT_PNMT_TEMT   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.4a  PDB: A:5-52 UniProt: 1-52            --------------------------------------------------------------------Exon 1.6c  PDB: A:121-261 UniProt: 121-263 [INCOMPLETE]                                                                                       Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.5a  PDB: A:52-121 UniProt: 52-121                              -------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2a14 A   5 FTGGDEYQKHFLPRDYLATYYSFDGSPSPEAEMLKFNLECLHKTFGPGGLQGDTLIDIGSGPTIYQVLAACDSFQDITLSDFTDRNREELEKWLKKEPGAYDWTPAVKFACELEGNSGRWEEKEEKLRAAVKRVLKCDVHLGNPLAPAVLPLADCVLTLLAMECACCSLDAYRAALCNLASLLKPGGHLVTTVTLRLPSYMVGKREFSCVALEKGEVEQAVLDAGFDIEQLLHSPQSYSVTNAANNGVCCIVARKKP 261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

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: Arylamine N-methyltransferase (40)

Protein domain: Indolethylamine N-methyltransferase, INMT (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2a14a1

A:5-261

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Human (Homo sapiens) (49)

2a14A00

A:5-261

(no "Pfam Domain" information available for 2A14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (INMT_HUMAN | O95050)

molecular function
	GO:0030748	amine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + an amine = S-adenosyl-L-homocysteine + a methylated amine.
	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:0004790	thioether S-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine(1+) + dimethyl sulfide = S-adenosyl-L-homocysteine + trimethylsulfonium.
	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:0009308	amine metabolic process	The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0009636	response to toxic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:150 - Pro A:151	[ RasMol ]

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