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Description

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

Authors :   A. Guelorget, B. Golinelli-Pimpaneau

Date :   25 Mar 10 (Deposition) - 12 May 10 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

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)

Compounds

Molecule 1 - SAM-DEPENDENT METHYLTRANSFERASE
	Chains	:	A
	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, PIMT-LIKE, PYRAB04300
	Organism Scientific	:	PYROCOCCUS ABYSSI
	Organism Taxid	:	29292
	Strain	:	GE5

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 12)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 48)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	EDO	24	Ligand/Ion	1,2-ETHANEDIOL
3	SAM	4	Ligand/Ion	S-ADENOSYLMETHIONINE
4	SO4	16	Ligand/Ion	SULFATE ION

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:75 , ILE A:76 , VAL A:77 , GLY A:101 , VAL A:102 , GLY A:103 , SER A:104 , GLY A:105 , ALA A:106 , LEU A:107 , GLU A:125 , ILE A:126 , ARG A:127 , PHE A:130 , LYS A:152 , ASP A:153 , ILE A:154 , TYR A:155 , ASP A:169 , HOH A:320 , HOH A:391 , HOH A:495	BINDING SITE FOR RESIDUE SAM A 301
02	AC2	SOFTWARE	LYS A:16 , ARG A:17 , LYS A:69 , HOH A:296 , HOH A:299 , HOH A:370 , HOH A:574 , HOH A:603	BINDING SITE FOR RESIDUE SO4 A 256
03	AC3	SOFTWARE	LYS A:49 , ARG A:127 , HOH A:497	BINDING SITE FOR RESIDUE SO4 A 257
04	AC4	SOFTWARE	PRO A:13 , ARG A:14 , LEU A:31 , HIS A:54 , HOH A:547	BINDING SITE FOR RESIDUE SO4 A 258
05	AC5	SOFTWARE	ARG A:42 , HOH A:369	BINDING SITE FOR RESIDUE SO4 A 259
06	AC6	SOFTWARE	MET A:215 , LYS A:216 , PHE A:249 , ALA A:250 , ARG A:251 , HOH A:444	BINDING SITE FOR RESIDUE EDO A 260
07	AC7	SOFTWARE	HIS A:78 , ARG A:218 , HOH A:445 , HOH A:513	BINDING SITE FOR RESIDUE EDO A 261
08	AC8	SOFTWARE	LEU A:67 , ASP A:68 , PRO A:79 , ALA A:87 , HOH A:414 , HOH A:516	BINDING SITE FOR RESIDUE EDO A 262
09	AC9	SOFTWARE	ILE A:63 , VAL A:86 , GLY A:90 , ILE A:91 , PHE A:110 , ASN A:113	BINDING SITE FOR RESIDUE EDO A 263
10	BC1	SOFTWARE	ALA A:131 , LYS A:132 , TRP A:135 , LEU A:151 , HOH A:422 , HOH A:559	BINDING SITE FOR RESIDUE EDO A 264
11	BC2	SOFTWARE	VAL A:77 , PRO A:79 , ALA A:82 , ALA A:106 , LEU A:107 , PHE A:110 , HOH A:569	BINDING SITE FOR RESIDUE EDO A 265
12	BC3	SOFTWARE	ARG A:60 , PRO A:186 , HOH A:283 , HOH A:303 , HOH A:430	BINDING SITE FOR RESIDUE ACT A 266

SS Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	A:196	-	A:233

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Ala A:100	-	Gly A:101

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 3MB5)

PROSITE Motifs (1, 1)

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_PYRAB	5-253	1	A:5-253

Biological Unit 1 (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

Exons (0, 0)

(no "Exon" information available for 3MB5)

Sequences/Alignments

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:255
 aligned with TRMI_PYRAB | Q9V1J7 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:255
                                                                                                                                                                                                                                                                                      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--   -
               SCOP domains d3mb5a_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains GCD14-3mb5A01 A:1-235                                                                                                                                                                                                                      -------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeee....eeee..eeee.hhhh......eee.....eeeee..hhhhhhhhh.......hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh....eeee..hhhhh.....eeeeee...hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhhhhhh...eee......eeee..eeee.........eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SAM_TRM61  PDB: A:5-253 UniProt: 5-253                                                                                                                                                                                                                   -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mb5 A   1 MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKSHKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEAGVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIKLKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQVMRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFARRILE 255
                                    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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric 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: 29292] (1)

d3mb5a_

CATH Domains (0, 0)

(no "CATH Domain" information available for 3MB5)

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: GCD14 (7)

Pyrococcus abyssi (strain GE5 / Orsay) (3)

GCD14-3mb5A01

A:1-235

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (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.

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	Cis Peptide Bonds
		Ala A:100 - Gly A:101	[ RasMol ]

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	TRMI_PYRAB \| Q9V1J7	:	3lga 3lhd

Related Entries Specified in the PDB File

3lga	THE SAME PROTEIN IN COMPLEX WITH SAH CRYSTALLIZED IN P31 SPACE GROUP
3lhd	THE SAME PROTEIN IN COMPLEX WITH SAH CRYSTALLIZED IN P212121 SPACE GROUP