2YXE - JenaLib

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Title :   CRYSTAL STRUCTURE OF L-ISOASPARTYL PROTEIN CARBOXYL METHYLTRANFERASE

Authors :   B. Padmanabhan, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   26 Apr 07 (Deposition) - 30 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Rossman-Type Fold, Alpha/Beta/Alpha Sandwich Structure, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Padmanabhan, Y. Bessho, S. Yokoyama
Crystal Structure Of L-Isoaspartyl Protein Carboxyl Methyltranferase
To Be Published
PubMed: search

Molecule 1 - PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.77
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21D
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PCM
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	243232
	Strain	:	DSM 2661
	Synonym	:	PROTEIN-BETA-ASPARTATE METHYLTRANSFERASE, PIMT, PROTEIN L- ISOASPARTYL METHYLTRANSFERASE, L-ISOASPARTYL PROTEIN CARBOXYL METHYLTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:186 , GLU A:188 , ILE A:195	BINDING SITE FOR RESIDUE ACT A 1001
2	AC2	SOFTWARE	GLU A:193 , LEU B:186 , GLU B:188 , ILE B:195	BINDING SITE FOR RESIDUE ACT B 2001

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

Asymmetric/Biological Unit

No.	Residues
1	Ala B:145	-	Pro B:146

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PCMT	PS01279	Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature.	PIMT_METJA	135-150	2	A:135-150 B:135-150

(no "Exon" information available for 2YXE)

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:214
 aligned with PIMT_METJA | Q57636 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
           PIMT_METJA     2 DLEEQKKAVIEKLIREGYIKSKRVIDALLKVPREEFLPEHLKEYAYVDTPLEIGYGQTISAIHMVGMMCELLDLKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDGTLGYEPLAPYDRIYTTAAGPKIPEPLIRQLKDGGKLLMPVGRYLQRLVLAEKRGDEIIIKDCGPVAFVPLVGKEGFQG 215
               SCOP domains d2yxea_ A: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 2yxeA00 A:2-215 Vaccinia Virus protein VP39                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..eee.hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeee....eeeeeeeee..eeeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------PCMT            ----------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yxe A   2 DLEEQKKAVIEKLIREGYIKSKRVIDALLKVPREEFLPEHLKEYAYVDTPLEIGYGQTISAIHMVGMMCELLDLKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDGTLGYEPLAPYDRIYTTAAGPKIPEPLIRQLKDGGKLLMPVGRYLQRLVLAEKRGDEIIIKDCGPVAFVPLVGKEGFQG 215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with PIMT_METJA | Q57636 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
           PIMT_METJA     2 DLEEQKKAVIEKLIREGYIKSKRVIDALLKVPREEFLPEHLKEYAYVDTPLEIGYGQTISAIHMVGMMCELLDLKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDGTLGYEPLAPYDRIYTTAAGPKIPEPLIRQLKDGGKLLMPVGRYLQRLVLAEKRGDEIIIKDCGPVAFVPLVGKEGFQ 214
               SCOP domains d2yxeb_ B: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains 2yxeB00 B:2-214 Vaccinia Virus protein VP39                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..eee.hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeee....eeeeeeeee..eeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------PCMT            ---------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yxe B   2 DLEEQKKAVIEKLIREGYIKSKRVIDALLKVPREEFLPEHLKEYAYVDTPLEIGYGQTISAIHMVGMMCELLDLKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDGTLGYEPLAPYDRIYTTAAGPKIPEPLIRQLKDGGKLLMPVGRYLQRLVLAEKRGDEIIIKDCGPVAFVPLVGKEGFQ 214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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)

Methanocaldococcus jannaschii [TaxId: 243232] (2)

1a	d2yxea_	A:
1b	d2yxeb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Methanocaldococcus jannaschii dsm 2661. Organism_taxid: 243232. Strain: dsm 2661. (1)

1a	2yxeA00	A:2-215
1b	2yxeB00	B:2-214

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PIMT_METJA | Q57636)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0004719	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + protein L-beta-aspartate = S-adenosyl-L-homocysteine + protein L-beta-aspartate methyl ester.
	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:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006479	protein methylation	The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
	GO:0030091	protein repair	The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues.
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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	Cis Peptide Bonds
		Ala B:145 - Pro B:146	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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