2CX8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF METHYLTRANSFERASE WITH LIGAND(SAH)

Authors :   K. Murayama, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   28 Jun 05 (Deposition) - 28 Dec 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.53

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

Keywords :   Methyltransferase, Type Iv, Rsgi, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Murayama, M. Shirouzu, S. Yokoyama
Crystal Structure Of Methyltransferase With Ligand(Sah)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - METHYL TRANSFERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:158 , HIS A:159 , VAL A:160 , VAL A:180 , GLY A:181 , PRO A:182 , GLU A:183 , GLY A:185 , PHE A:186 , VAL A:202 , LEU A:204 , GLY A:205 , ARG A:207 , ILE A:208 , LEU A:209 , ALA A:214	BINDING SITE FOR RESIDUE SAH A 300
2	AC2	SOFTWARE	ALA B:158 , HIS B:159 , VAL B:180 , GLY B:181 , PRO B:182 , GLU B:183 , GLY B:184 , GLY B:185 , LEU B:204 , GLY B:205 , ARG B:207 , LEU B:209 , ALA B:214 , HOH B:436	BINDING SITE FOR RESIDUE SAH B 400

(no "SS Bond" information available for 2CX8)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:52	-	Pro A:53
2	Pro A:53	-	Pro A:54

(no "SAP(SNP)/Variant" information available for 2CX8)

(no "PROSITE Motif" information available for 2CX8)

(no "Exon" information available for 2CX8)

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:225
 aligned with Q5SKI6_THET8 | Q5SKI6 from UniProtKB/TrEMBL  Length:228

    Alignment length:225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
         Q5SKI6_THET8     4 HRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEMGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
               SCOP domains d2cx8a1 A:4-66 Hypothetical protein TTHA0657 (TT1575)          d2cx8a2 A:67-228 Hypothetical protein TTHA0657 (TT1575)                                                                                                            SCOP domains
               CATH domains 2cx8A01 A:4-66 Hypothetical PUA domain-like; domain 1          2cx8A02 A:67-228  [code=3.40.1280.10, no name defined]                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........hhhhhhhhhhh.......eeeee....eeeeeeee.....eeeeeeee.........eeeeee....hhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhh......ee...ee.hhh.....eeee......hhhhh......eeeee......hhhhhhhhhhhheeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx8 A   4 HRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEmGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
                                                                                                                                       113-MSE

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q5SKI6_THET8 | Q5SKI6 from UniProtKB/TrEMBL  Length:228

    Alignment length:173
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
         Q5SKI6_THET8    56 RYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEMGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
               SCOP domains -----------d2cx8b1 B:67-228 Hypothetical protein TTHA0657 (TT1575)                                                                                                            SCOP domains
               CATH domains -----------2cx8B01 B:67-228  [code=3.40.1280.10, no name defined]                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee....hhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhh.....ee...ee.hhh.....eeee......hhhhhh.....eeeee......hhhhhhhhhhhheeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx8 B  56 RYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEmGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
                                                                                   113-MSE

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Alpha/beta knot (33)

Homologous Superfamily: [code=3.40.1280.10, no name defined] (33)

Thermus thermophilus. Organism_taxid: 274. (4)

1a	2cx8A02	A:67-228
1b	2cx8B01	B:67-228

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Ribosomal Protein L25; Chain P (96)

Homologous Superfamily: Hypothetical PUA domain-like; domain 1 (7)

Thermus thermophilus. Organism_taxid: 274. (2)

2cx8A01

A:4-66

(no "Pfam Domain" information available for 2CX8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q5SKI6_THET8 | Q5SKI6)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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		Pro A:53 - Pro A:54	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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