2EJU - JenaLib

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Title :   COMPLEX STRUCTURE OF TRM1 FROM PYROCOCCUS HORIKOSHII WITH S-ADENOSYL-L-HOMOCYSTEIN

Authors :   Ihsanawati, M. Shirouzu, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   20 Mar 07 (Deposition) - 25 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Trna Modification Enzyme, Guanine-26, N(2)-N(2)-Dimethyltransferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Ihsanawati, M. Nishimoto, K. Higashijima, M. Shirouzu, H. Grosjean, Y. Bessho, S. Yokoyama
Crystal Structure Of Trna N(2), N(2)-Guanosine Dimethyltransferase Trm1 From Pyrococcus Horikoshii
J. Mol. Biol. V. 383 871 2008
PubMed-ID: 18789948 | Reference-DOI: 10.1016/J.JMB.2008.08.068

Molecule 1 - N(2),N(2)-DIMETHYLGUANOSINE TRNA METHYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.1.1.32
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-378
	Gene	:	TRM1
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953
	Synonym	:	TRNA(GUANINE-26,N(2)-N(2))METHYLTRANSFERASE, TRNA 2,2- DIMETHYLGUANOSINE-26 METHYLTRANSFERASE, TRNA(M(2,2)G26) DIMETHYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 4)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:36 , LEU A:55 , ALA A:57 , ILE A:60 , ARG A:61 , ASN A:77 , ASP A:78 , ILE A:79 , SER A:80 , ASP A:119 , ASP A:120 , ALA A:121 , ASP A:138 , PHE A:140 , PHE A:146 , HOH A:618 , HOH A:623 , HOH A:640 , HOH A:750 , HOH A:795 , HOH A:864 , HOH A:894	BINDING SITE FOR RESIDUE SAH A 501
2	AC2	SOFTWARE	ALA A:220 , LEU A:281 , LYS A:282 , ILE A:312 , GLU A:315 , LEU A:316 , ASP A:317 , HIS A:356 , HOH A:642	BINDING SITE FOR RESIDUE GOL A 601

Asymmetric Unit

No.	Residues
1	A:171	-	A:192

Asymmetric Unit

No.	Residues
1	Gly A:274	-	Pro A:275

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TRM1	PS51626	Trm1 methyltransferase domain profile.	TRM1_PYRHO	7-378	1	A:4-375

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TRM1	PS51626	Trm1 methyltransferase domain profile.	TRM1_PYRHO	7-378	1	A:4-375

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TRM1	PS51626	Trm1 methyltransferase domain profile.	TRM1_PYRHO	7-378	2	A:4-375

(no "Exon" information available for 2EJU)

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
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Chain A from PDB  Type:PROTEIN  Length:371
 aligned with TRM1_PYRHO | O59493 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:375
                                    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       295       305       315       325       335       345       355       365       375     
           TRM1_PYRHO     6 LIEVQEGKAKILIPKAESIYDSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRRLKIETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIKR 380
               SCOP domains d2ejua_ A: N(2),    N(2)-dimethylguanosine tRNA methyltransferase Trm1                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee...----......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh......ee...eeeee...eeeeee.hhhhhhhhh...eeeeee.....hhhhhhhhhhheeeeeeeeeee.hhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeehhhhhhhhhh.eeeeee......eeeee.........eeeee.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......eehhhhhhhhh....hhhhhhhhhhhh...eeee..eeeeeee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_MT_TRM1  PDB: A:4-375 UniProt: 7-378                                                                                                                                                                                                                                                                                                                                            -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eju A   3 LIEVQEGKAKILIPKA----DSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRRLKIETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIKR 377
                                    12     |   -|       32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372     
                                          18   23

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 2EJU)

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

Asymmetric Unit(hide GO term definitions)

Chain A (TRM1_PYRHO | O59493)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0004809	tRNA (guanine-N2-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + tRNA containing guanine = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	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.

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	Cis Peptide Bonds
		Gly A:274 - Pro A:275	[ RasMol ]

Biological Units
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	2eju
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	TRM1_PYRHO \| O59493
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	2.1.1.32
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	TRM1_PYRHO \| O59493
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UniProtKB/Swiss-Prot
	TRM1_PYRHO \| O59493	:	2dul 2ejt 2ytz

2dul	THE SAME PROTEIN BUT WITHOUT LIGAND
2ejt	THE SAME PROTEIN WITH S-ADENOSYL-L-METHIONINE RELATED ID: PHO001001829.3 RELATED DB: TARGETDB

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SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

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