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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF P. ABYSSI TRNA M1A58 METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE

Authors :   A. Guelorget, B. Golinelli-Pimpaneau, J. Wouters, C. Barbey

Date :   22 Jan 10 (Deposition) - 19 May 10 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.59

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

Keywords :   Rna Methyltransferase, M1A, Trmi, Intermolecular Contacts, Region- Specificity, Tetramer, Disulfide Bond, Hyperthermostability, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Guelorget, M. Roovers, V. Guerineau, C. Barbey, X. Li, B. Golinelli-Pimpaneau
Insights Into The Hyperthermostability And Unusual Region-Specificity Of Archaeal Pyrococcus Abyssi Trna M1A57/58 Methyltransferase.
Nucleic Acids Res. V. 38 6206 2010
PubMed-ID: 20483913 | Reference-DOI: 10.1093/NAR/GKQ381
(for further references see the PDB file header)

Molecule 1 - SAM-DEPENDENT METHYLTRANSFERASE, PUTATIVE
	Chains	:	C, A, B, D
	EC Number	:	2.1.1.36
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30
	Expression System Strain	:	ROSETTA DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PAB0283
	Organism Scientific	:	PYROCOCCUS ABYSSI
	Organism Taxid	:	272844
	Strain	:	GE5

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY C:101 , GLY C:103 , GLU C:125 , ILE C:126 , PHE C:130 , LYS C:152 , ASP C:153 , ILE C:154 , TYR C:155 , PRO C:195 , HOH C:276	BINDING SITE FOR RESIDUE SAH C 301
2	AC2	SOFTWARE	GLY A:101 , GLY A:103 , GLU A:125 , ILE A:126 , PHE A:130 , ASP A:153 , ILE A:154 , TYR A:155 , ASP A:169 , PRO A:171	BINDING SITE FOR RESIDUE SAH A 301
3	AC3	SOFTWARE	GLY B:101 , GLY B:103 , GLU B:125 , ILE B:126 , PHE B:130 , LYS B:152 , ASP B:153 , ILE B:154 , TYR B:155 , ASP B:169 , LEU B:170 , HOH B:271 , HOH B:277	BINDING SITE FOR RESIDUE SAH B 301
4	AC4	SOFTWARE	GLY D:101 , GLY D:103 , GLU D:125 , ILE D:126 , ARG D:127 , PHE D:130 , ASP D:153 , ILE D:154 , TYR D:155 , ASP D:169 , LEU D:170 , PRO D:171 , PRO D:195 , GLN D:199	BINDING SITE FOR RESIDUE SAH D 301

Asymmetric/Biological Unit

No.	Residues
1	B:196	-	D:233
2	B:233	-	D:196
3	C:196	-	A:233
4	C:233	-	A:196

Asymmetric/Biological Unit

No.	Residues
1	Pro C:74	-	Gln C:75
2	Pro B:74	-	Gln B:75

(no "SAP(SNP)/Variant" information available for 3LHD)

Asymmetric/Biological Unit (1, 4)

	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_PYRAB	5-253	4	A:5-253 B:5-253 C:5-253 D:5-253

(no "Exon" information available for 3LHD)

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:253
 aligned with TRMI_PYRAB | Q9V1J7 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           TRMI_PYRAB     1 MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKSHKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQVMRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFARRI 253
               SCOP domains d3lhda_ A: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeee.........................eee.....eeeee..hhhhhhhhh.......hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh.eeeee...........eeeeee...hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh.......eeeeeeeeeeeee..eeee..eee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SAM_TRM61  PDB: A:5-253 UniProt: 5-253                                                                                                                                                                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lhd A   1 MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKSHKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQVMRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFARRI 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with TRMI_PYRAB | Q9V1J7 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           TRMI_PYRAB     1 MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKSHKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQVMRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFARRI 253
               SCOP domains d3lhdb_ B: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeee....ee......ee.hhh.......eee.....eeeee..hhhhhhhh........hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh.....eeeeee...hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh.......eeeeeeeeeeee....eee..eee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SAM_TRM61  PDB: B:5-253 UniProt: 5-253                                                                                                                                                                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lhd B   1 MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKSHKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQVMRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFARRI 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain C from PDB  Type:PROTEIN  Length:253
 aligned with TRMI_PYRAB | Q9V1J7 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           TRMI_PYRAB     1 MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKSHKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQVMRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFARRI 253
               SCOP domains d3lhdc_ C: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeee....eeee..eeee.hhhh......eee.....eeeee..hhhhhhhhh.......hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....eeeeee...hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh.......eeeeeeeeeee......ee..eee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SAM_TRM61  PDB: C:5-253 UniProt: 5-253                                                                                                                                                                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lhd C   1 MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKSHKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQVMRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFARRI 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain D from PDB  Type:PROTEIN  Length:253
 aligned with TRMI_PYRAB | Q9V1J7 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           TRMI_PYRAB     1 MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKSHKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQVMRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFARRI 253
               SCOP domains d3lhdd_ D: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) GCD14-3lhdD01 D:1-235                                                                                                                                                                                                                      ------------------ Pfam domains (1)
           Pfam domains (2) GCD14-3lhdD02 D:1-235                                                                                                                                                                                                                      ------------------ Pfam domains (2)
           Pfam domains (3) GCD14-3lhdD03 D:1-235                                                                                                                                                                                                                      ------------------ Pfam domains (3)
           Pfam domains (4) GCD14-3lhdD04 D:1-235                                                                                                                                                                                                                      ------------------ Pfam domains (4)
         Sec.struct. author ......eeeee.....eeeee....eeee..eeee.hhhh......eee.....eeeee..hhhhhhhhh.......hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh....eeee..hhhhh.....eeeeee...hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee....eee..eee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SAM_TRM61  PDB: D:5-253 UniProt: 5-253                                                                                                                                                                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lhd D   1 MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKSHKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQVMRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFARRI 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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: automated matches (94)

Protein domain: automated matches (94)

Pyrococcus abyssi [TaxId: 272844] (2)

1a	d3lhda_	A:
1b	d3lhdb_	B:
1c	d3lhdc_	C:
1d	d3lhdd_	D:

(no "CATH Domain" information available for 3LHD)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: GCD14 (7)

Pyrococcus abyssi (strain GE5 / Orsay) (3)

1a	GCD14-3lhdD01	D:1-235
1b	GCD14-3lhdD02	D:1-235
1c	GCD14-3lhdD03	D:1-235
1d	GCD14-3lhdD04	D:1-235

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (TRMI_PYRAB | Q9V1J7)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Pro B:74 - Gln B:75	[ RasMol ]
		Pro C:74 - Gln C:75	[ RasMol ]

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	3lhd
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	2.1.1.36
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	TRMI_PYRAB \| Q9V1J7	:	3lga 3mb5

3lga	THE SAME PROTEIN CRYSTALLIZED IN ANOTHER SPACE GROUPE P31

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

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