2YTZ - JenaLib

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Title :   COMPLEX STRUCTURE OF TRM1 FROM PYROCOCCUS HORIKOSHII WITH S-ADENOSYL-L-HOMOCYSTEIN IN THE ORTHORHOMBIC CRYSTAL-LATTICE

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

Date :   05 Apr 07 (Deposition) - 09 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

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 (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
(for further references see the PDB file header)

Molecule 1 - N(2),N(2)-DIMETHYLGUANOSINE TRNA METHYLTRANSFERASE
	Chains	:	A, B
	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	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

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

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:129 , ARG A:130 , ARG A:156 , HOH B:1071	BINDING SITE FOR RESIDUE SO4 A 1004
2	AC2	SOFTWARE	HIS A:174 , PRO A:175 , ARG A:176 , ALA A:177	BINDING SITE FOR RESIDUE SO4 A 1005
3	AC3	SOFTWARE	LYS A:337 , VAL A:338 , GLU A:339 , ARG A:354 , HOH A:1162	BINDING SITE FOR RESIDUE SO4 A 1007
4	AC4	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 , GLN A:348 , HOH A:1009 , HOH A:1012 , HOH A:1030 , HOH A:1043 , HOH A:1095 , HOH A:1100	BINDING SITE FOR RESIDUE SAH A 1001
5	AC5	SOFTWARE	HIS B:174 , PRO B:175 , ARG B:176 , ALA B:177 , HOH B:1046	BINDING SITE FOR RESIDUE SO4 B 1003
6	AC6	SOFTWARE	PHE B:27 , ARG B:36 , LEU B:55 , ALA B:57 , ILE B:60 , ARG B:61 , ASP B:78 , ILE B:79 , SER B:80 , ASP B:119 , ASP B:120 , ALA B:121 , ASP B:138 , PHE B:140 , PHE B:146 , HOH B:1013 , HOH B:1030 , HOH B:1037 , HOH B:1116	BINDING SITE FOR RESIDUE SAH B 1002

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

Asymmetric Unit

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

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

Asymmetric Unit (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 B: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, 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	- B:4-375

Biological Unit 3 (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 B:4-375

(no "Exon" information available for 2YTZ)

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:371
 aligned with TRM1_PYRHO | O59493 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:376
                                    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       264       274       284       294       304       314       324       334       344       354       364       374      
           TRM1_PYRHO     5 ELIEVQEGKAKILIPKAESIYDSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRRLKIETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIKR 380
               SCOP domains d2ytza_ A: N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee............hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....eee..eeeee...eeeeee.hhhhhhhhh...eeeeee.....hhhhhhhhhhheeeeeeeeeee.hhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeeehhhhhhhhhh.eeeeee......eeeee.........eeeee.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......eehhhhhhh-----.hhhhhhhhhhhh...eeee..eeeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SAM_MT_TRM1  PDB: A:4-375 UniProt: 7-378                                                                                                                                                                                                                                                                                                                                            -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ytz A   2 ELIEVQEGKAKILIPKAESIYDSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRR-----KKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIKR 377
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321        |-    |  341       351       361       371      
                                                                                                                                                                                                                                                                                                                                                                  330   336

Chain B from PDB  Type:PROTEIN  Length:365
 aligned with TRM1_PYRHO | O59493 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:374
                                    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 LIEVQEGKAKILIPKAESIYDSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRRLKIETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIK 379
               SCOP domains d2ytzb_ B: N(2      ),N(2)-dimethylguanosine tRNA methyltransferase Trm1                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------TRM-2ytz      B01 B:9-376                                                                                                                                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) ------TRM-2ytz      B02 B:9-376                                                                                                                                                                                                                                                                                                                                                        Pfam domains (2)
         Sec.struct. author .eeee....eeee.------......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh......eee..eeee....eeeeee.hhhhhhhhh...eeeeee.....hhhhhhhhhhheeeeeeeeeee.hhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeehhhhhhhhhh.eeeeee......eeeee.........eeeee.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......eehhhhhhh---...hhhhhhhhhhhh...eeee..eeeeeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_MT_TRM1  PDB: B:4-375 UniProt: 7-378                                                                                                                                                                                                                                                                                                                                            - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ytz B   3 LIEVQEGKAKILIP------DSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRR---ETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIK 376
                                    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       | - |     342       352       362       372    
                                        16     23                                                                                                                                                                                                                                                                                                                330 334

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 2YTZ)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: TRM (1)

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (1)

1a	TRM-2ytzB01	B:9-376
1b	TRM-2ytzB02	B:9-376

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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

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

2dul	THE SAME PROTEIN BUT WITHOUT LIGAND
2ejt	THE SAME PROTEIN WITH SAM
2eju	THE SAME PROTEIN WITH SAH IN THE CENTERED ORTHORHOMBIC CRYSTAL LATTICE RELATED ID: PHO001001829.5 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

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