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Title :   CRYSTAL STRUCTURE OF HUMAN METHYLTRANSFERASE AD-003 IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE

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

Date :   07 Nov 05 (Deposition) - 15 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A,B

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

Reference :   J. Min, H. Wu, H. Zeng, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
The Crystal Structure Of Human Ad-003 Protein In Complex With S-Adenosyl-L-Homocysteine
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ADRENAL GLAND PROTEIN AD-003
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P28A-LIC
	Expression System Strain	:	E.COLI BL21 (DE3) CODON PLUS RIL (STRATAGENE)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:20 , MET A:30 , GLY A:70 , GLY A:72 , ARG A:75 , ILE A:76 , ASP A:92 , ILE A:93 , THR A:94 , PHE A:97 , CYS A:118 , GLY A:119 , LEU A:120 , GLN A:121 , GLN A:136 , TRP A:137 , VAL A:138 , HIS A:141 , HOH A:1404 , HOH A:1408 , HOH A:1410	BINDING SITE FOR RESIDUE SAH A 1401
2	AC2	SOFTWARE	TRP B:20 , MET B:30 , GLY B:70 , GLY B:72 , ARG B:75 , ILE B:76 , ASP B:92 , ILE B:93 , THR B:94 , PHE B:97 , GLY B:119 , LEU B:120 , GLN B:121 , GLN B:136 , TRP B:137 , VAL B:138 , HIS B:141 , HOH B:1404 , HOH B:1409 , HOH B:1411	BINDING SITE FOR RESIDUE SAH B 1402

(no "SS Bond" information available for 2EX4)

(no "Cis Peptide Bond" information available for 2EX4)

(no "SAP(SNP)/Variant" information available for 2EX4)

(no "PROSITE Motif" information available for 2EX4)

Asymmetric/Biological Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000372486	1	ENSE00001457925	chr9:132371163-132371457	295	NTM1A_HUMAN	-	0	0	-	-
1.6b	ENST00000372486	6b	ENSE00001457923	chr9:132394929-132395144	216	NTM1A_HUMAN	1-54	54	2	A:1-54 B:1-54	54 54
1.7b	ENST00000372486	7b	ENSE00000984438	chr9:132396333-132396585	253	NTM1A_HUMAN	55-139	85	2	A:60-140 B:60-140	81 81
1.8e	ENST00000372486	8e	ENSE00001457921	chr9:132397487-132398209	723	NTM1A_HUMAN	139-223	85	2	A:140-224 B:140-224	85 85

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
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Chain A from PDB  Type:PROTEIN  Length:221
 aligned with NTM1A_HUMAN | Q9BV86 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:225
                              1                                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218     
          NTM1A_HUMAN     - --MTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR 223
               SCOP domains ---d2ex4a1 A:2-224 Adrenal gland protein AD-003 (C9orf32    )                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhh----.....eeeee....hhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh.eeeeee.hhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeee....eeee....eeeehhhhhhhhhhhh..eeeeeee.........eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.6b  PDB: A:1-54 UniProt: 1-54                  Exon 1.7b  PDB: A:60-140 UniProt: 55-139 [INCOMPLETE]                                ------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8e  PDB: A:140-224 UniProt: 139-223                                            Transcript 1 (2)
                 2ex4 A  -1 RGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLR----KTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR 224
                                     8        18        28        38        48     |   -|       69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
                                                                                  54   60

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with NTM1A_HUMAN | Q9BV86 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:225
                              1                                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218     
          NTM1A_HUMAN     - --MTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR 223
               SCOP domains d2ex4b_ B: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..hhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhh----.....eeeee....hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh.eeeeee.hhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeeee...eeee....eeeeehhhhhhhhhhh..eeeeeee.........eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.6b  PDB: B:1-54 UniProt: 1-54                  Exon 1.7b  PDB: B:60-140 UniProt: 55-139 [INCOMPLETE]                                ------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8e  PDB: B:140-224 UniProt: 139-223                                            Transcript 1 (2)
                 2ex4 B  -1 RGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLR----KTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR 224
                                     8        18        28        38        48     |   -|       69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
                                                                                  54   60

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 '\|'

(no "CATH Domain" information available for 2EX4)

(no "Pfam Domain" information available for 2EX4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NTM1A_HUMAN | Q9BV86)

molecular function
	GO:0071885	N-terminal protein N-methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to the alpha-amino group of the N-terminal amino or imino acid residue of a protein substrate. For example, yeast Tae1p and mammalian family member METTL11A preferentially modify the N-terminal residue of substrates with the N-terminal sequence X-Pro-Lys, where X can be Pro, Ala, or Ser.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0008276	protein methyltransferase activity	Catalysis of the transfer of a methyl group (CH3-) to a protein.
	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:0018011	N-terminal peptidyl-alanine methylation	The methylation of the N-terminal alanine of proteins.
	GO:0018012	N-terminal peptidyl-alanine trimethylation	The trimethylation of the N-terminal alanine of proteins to form the derivative peptidyl-N,N,N-trimethyl-L-alanine.
	GO:0018016	N-terminal peptidyl-proline dimethylation	The methylation of the N-terminal proline of proteins to form the derivative N,N-dimethyl-L-proline.
	GO:0035572	N-terminal peptidyl-serine dimethylation	The dimethylation of the N-terminal serine of proteins to form the derivative N,N-dimethylserine.
	GO:0035573	N-terminal peptidyl-serine trimethylation	The trimethylation of the N-terminal serine of proteins to form the derivative N,N,N-trimethylserine.
	GO:0006480	N-terminal protein amino acid methylation	The methylation of the N-terminal amino acid of a protein.
	GO:0007059	chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0007051	spindle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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