1I9G - JenaLib

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Title :   CRYSTAL STRUCTURE OF AN ADOMET DEPENDENT METHYLTRANSFERASE

Authors :   A. Gupta, P. H. Kumar, T. K. Dineshkumar, U. Varshney, H. S. Subramanya, Structural Genomics Consortium (Tbsgc)

Date :   20 Mar 01 (Deposition) - 26 Sep 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

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

Keywords :   Mycobacterium, Mtase, Adomet, Crystal, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Gupta, P. H. Kumar, T. K. Dineshkumar, U. Varshney, H. S. Subramanya
Crystal Structure Of Rv2118C: An Adomet-Dependent Methyltransferase From Mycobacterium Tuberculosis H37Rv.
J. Mol. Biol. V. 312 381 2001
PubMed-ID: 11554794 | Reference-DOI: 10.1006/JMBI.2001.4935

Molecule 1 - HYPOTHETICAL PROTEIN RV2118C
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PQE60
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RV2118C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	SAM	4	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:81 , VAL A:82 , ILE A:83 , GLY A:107 , ALA A:108 , GLY A:109 , SER A:110 , GLY A:111 , ALA A:112 , LEU A:113 , GLU A:131 , GLN A:132 , ARG A:133 , HIS A:136 , SER A:160 , ASP A:161 , LEU A:162 , ASP A:178 , MET A:179 , VAL A:185 , HOH A:337 , HOH A:386 , HOH A:389 , HOH A:405	BINDING SITE FOR RESIDUE SAM A 301

(no "SS Bond" information available for 1I9G)

(no "Cis Peptide Bond" information available for 1I9G)

(no "SAP(SNP)/Variant" information available for 1I9G)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_TRM61	PS51620	tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.	TRMI_MYCTO	10-261	1	A:10-261
1	SAM_TRM61	PS51620		TRMI_MYCTU	10-261	1	A:10-261

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_TRM61	PS51620	tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.	TRMI_MYCTO	10-261	1	A:10-261
1	SAM_TRM61	PS51620		TRMI_MYCTU	10-261	1	A:10-261

Biological Unit 2 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_TRM61	PS51620	tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.	TRMI_MYCTO	10-261	4	A:10-261
1	SAM_TRM61	PS51620		TRMI_MYCTU	10-261	4	A:10-261

(no "Exon" information available for 1I9G)

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:264
 aligned with TRMI_MYCTO | P9WFZ0 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:264
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    
           TRMI_MYCTO     4 TGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVVKSSNGALFLVLRPLLVDYVMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDGSVDRAVLDMLAPWEVLDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQCWTEPRAWETLQRGWNVVGLAVRPQHSMRGHTAFLVATRRLAPGAVA 267
               SCOP domains d1i9ga_ A: Probable methyltransferase Rv2118c                                                                                                                                                                                                                            SCOP domains
               CATH domains 1i9gA01 A:4-67  [code=3.10.330.20, no name defined]             1i9gA02 A:68-231,A:248-267 Vaccinia Virus protein VP39                                                                                                              ----------------1i9gA02              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee....eeeee.....eeee..eeeehhhhh.....eeee.....eeeee..hhhhhhh.........hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh.....eeee..hhhhh......eeeeeee..hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhhh.....eee......eeee..eeee.........eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------SAM_TRM61  PDB: A:10-261 UniProt: 10-261                                                                                                                                                                                                                    ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1i9g A   4 TGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVVKSSNGALFLVLRPLLVDYVMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDGSVDRAVLDMLAPWEVLDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQCWTEPRAWETLQRGWNVVGLAVRPQHSMRGHTAFLVATRRLAPGAVA 267
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

Chain A from PDB  Type:PROTEIN  Length:264
 aligned with TRMI_MYCTU | P9WFZ1 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:264
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    
           TRMI_MYCTU     4 TGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVVKSSNGALFLVLRPLLVDYVMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDGSVDRAVLDMLAPWEVLDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQCWTEPRAWETLQRGWNVVGLAVRPQHSMRGHTAFLVATRRLAPGAVA 267
               SCOP domains d1i9ga_ A: Probable methyltransferase Rv2118c                                                                                                                                                                                                                            SCOP domains
               CATH domains 1i9gA01 A:4-67  [code=3.10.330.20, no name defined]             1i9gA02 A:68-231,A:248-267 Vaccinia Virus protein VP39                                                                                                              ----------------1i9gA02              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee....eeeee.....eeee..eeeehhhhh.....eeee.....eeeee..hhhhhhh.........hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh.....eeee..hhhhh......eeeeeee..hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhhh.....eee......eeee..eeee.........eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------SAM_TRM61  PDB: A:10-261 UniProt: 10-261                                                                                                                                                                                                                    ------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1i9g A   4 TGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVVKSSNGALFLVLRPLLVDYVMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDGSVDRAVLDMLAPWEVLDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQCWTEPRAWETLQRGWNVVGLAVRPQHSMRGHTAFLVATRRLAPGAVA 267
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Mycobacterium tuberculosis. Organism_taxid: 1773. (7)

1i9gA02

A:68-231,A:248-267

Architecture: Roll (3276)

Topology: Vcp-like ATPase; Chain A, domain 2 (12)

Homologous Superfamily: [code=3.10.330.20, no name defined] (2)

Mycobacterium tuberculosis. Organism_taxid: 1773. (1)

1i9gA01

A:4-67

(no "Pfam Domain" information available for 1I9G)

Asymmetric Unit(hide GO term definitions)

Chain A (TRMI_MYCTO | P9WFZ0)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0016429	tRNA (adenine-N1-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methyladenine.
	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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0030488	tRNA methylation	The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0031515	tRNA (m1A) methyltransferase complex	A protein complex involved in the catalysis of the formation of the modified nucleotide 1-methyladenosine (m1A) in tRNA. In yeast, it is a heterotetramer of two subunits, Gcd10p and Gcd14p, while in bacteria and archaea it is a homotetramer.

Chain A (TRMI_MYCTU | P9WFZ1)

molecular function
	GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0016429	tRNA (adenine-N1-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methyladenine.
	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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0030488	tRNA methylation	The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0031515	tRNA (m1A) methyltransferase complex	A protein complex involved in the catalysis of the formation of the modified nucleotide 1-methyladenosine (m1A) in tRNA. In yeast, it is a heterotetramer of two subunits, Gcd10p and Gcd14p, while in bacteria and archaea it is a homotetramer.

Asymmetric Unit
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