4DF3 - JenaLib

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Title :   CRYSTAL STRUCTURE OF AEROPYRUM PERNIX FIBRILLARIN IN COMPLEX WITH NATIVELY BOUND S-ADENOSYL-L-METHIONINE AT 1.7A

Authors :   U. De Silva

Date :   22 Jan 12 (Deposition) - 08 Aug 12 (Release) - 20 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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

Keywords :   Nadp Rossmann Superfamily, Methyltransferase, S-Adenosyl-L-Methionine (Sam) Binding, Nucleolus, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. De Silva, Z. Zhou, B. A. Brown
Structure Of Aeropyrum Pernix Fibrillarin In Complex With Natively Bound S-Adenosyl-L-Methionine At 1. 7 A Resolution.
Acta Crystallogr. , Sect. F V. 68 854 2012
PubMed-ID: 22869109 | Reference-DOI: 10.1107/S1744309112026528

Molecule 1 - FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	FLPA, APE_2196
	Mutation	:	YES
	Organism Scientific	:	AEROPYRUM PERNIX
	Organism Taxid	:	56636

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SAM	2	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, 1)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:83 , GLY A:85 , ALA A:87 , THR A:90 , THR A:91 , GLU A:109 , PHE A:110 , GLY A:133 , ASP A:134 , ALA A:135 , ASP A:154 , VAL A:155 , GLN A:157 , HOH A:409 , HOH A:411 , HOH A:413 , HOH A:436 , HOH A:458 , HOH A:490	BINDING SITE FOR RESIDUE SAM A 301
2	AC2	SOFTWARE	TYR B:83 , GLY B:85 , ALA B:87 , THR B:90 , THR B:91 , GLU B:109 , PHE B:110 , GLY B:133 , ASP B:134 , ALA B:135 , ASP B:154 , VAL B:155 , GLN B:157 , HOH B:402 , HOH B:405 , HOH B:424 , HOH B:453	BINDING SITE FOR RESIDUE SAM B 301

(no "SS Bond" information available for 4DF3)

Asymmetric Unit

No.	Residues
1	Asp A:218	-	Pro A:219
2	Asp B:218	-	Pro B:219

(no "SAP(SNP)/Variant" information available for 4DF3)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIBRILLARIN	PS00566	Fibrillarin signature.	FLPA_AERPE	103-117	2	A:103-117 B:103-117

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIBRILLARIN	PS00566	Fibrillarin signature.	FLPA_AERPE	103-117	1	A:103-117 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIBRILLARIN	PS00566	Fibrillarin signature.	FLPA_AERPE	103-117	1	- B:103-117

(no "Exon" information available for 4DF3)

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:230
 aligned with FLPA_AERPE | Q9Y9U3 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           FLPA_AERPE     1 MVEVVSVREHDRWRGVYVVELEDGSLRIATKNLVPGQRVYGERIFRYNGEEYREWNAYRSKLAAALLKGLIELPVKEGDRILYLGIASGTTASHMSDIIGPRGRIYGVEFAPRVMRDLLTVVRDRRNIFPILGDARFPEKYRHLVEGVDGLYADVAQPEQAAIVVRNARFFLRDGGYMLMAIKARSIDVTTEPSEVYKREIKTLMDGGLEIKDVVHLDPFDRDHAMIYAV 230
               SCOP domains d4df3a_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......eeeeee....eeeeee............eeee..eeeee.....hhhhhhhhh...........eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh.....eeeee....hhhhhh.....eeeeee.....hhhhhhhhhhhhheeeeeeeeeeee.hhhhhhh..hhhhhhhhhhhhhh..eeeeeee.......eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------FIBRILLARIN    ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4df3 A   1 MVEVVSVSRHDRWRGVYVVELEDGSLRIATKNLVPGQRVYGERIFRYNGEEYREWNAYRSKLAAALLKGLIELPVKEGDRILYLGIASGTTASHMSDIIGPRGRIYGVEFAPRVMRDLLTVVRDRRNIFPILGDARFPEKYRHLVEGVDGLYADVAQPEQAAIVVRNARFFLRDGGYMLMAIKARSIDVTTEPSEVYKREIKTLMDGGLEIKDVVHLDPFDRDHAMIYAV 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:230
 aligned with FLPA_AERPE | Q9Y9U3 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           FLPA_AERPE     1 MVEVVSVREHDRWRGVYVVELEDGSLRIATKNLVPGQRVYGERIFRYNGEEYREWNAYRSKLAAALLKGLIELPVKEGDRILYLGIASGTTASHMSDIIGPRGRIYGVEFAPRVMRDLLTVVRDRRNIFPILGDARFPEKYRHLVEGVDGLYADVAQPEQAAIVVRNARFFLRDGGYMLMAIKARSIDVTTEPSEVYKREIKTLMDGGLEIKDVVHLDPFDRDHAMIYAV 230
               SCOP domains d4df3b_ B: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......eeeeee....eeeeee............eeee..eeeee.....hhhhhhhhhh..........eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeeee....hhhhhh.....eeeeee.....hhhhhhhhhhhhheeeeeeeeeeee.hhhhhh...hhhhhhhhhhhhhh...eeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------FIBRILLARIN    ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4df3 B   1 MVEVVSVSRHDRWRGVYVVELEDGSLRIATKNLVPGQRVYGERIFRYNGEEYREWNAYRSKLAAALLKGLIELPVKEGDRILYLGIASGTTASHMSDIIGPRGRIYGVEFAPRVMRDLLTVVRDRRNIFPILGDARFPEKYRHLVEGVDGLYADVAQPEQAAIVVRNARFFLRDGGYMLMAIKARSIDVTTEPSEVYKREIKTLMDGGLEIKDVVHLDPFDRDHAMIYAV 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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(

)

Folds(

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Superfamilies( (-)

)

Families(

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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)

Aeropyrum pernix [TaxId: 56636] (1)

1a	d4df3a_	A:
1b	d4df3b_	B:

(no "CATH Domain" information available for 4DF3)

(no "Pfam Domain" information available for 4DF3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (FLPA_AERPE | Q9Y9U3)

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: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:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	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
		Asp A:218 - Pro A:219	[ RasMol ]
		Asp B:218 - Pro B:219	[ RasMol ]

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