1JG3 - JenaLib

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Title :   CRYSTAL STRUCTURE OF L-ISOASPARTYL (D-ASPARTYL) O-METHYLTRANSFERASE WITH ADENOSINE & VYP(ISP)HA SUBSTRATE

Authors :   S. C. Griffith, M. R. Sawaya, D. Boutz, N. Thapar, J. Katz, S. Clarke, T. O

Date :   22 Jun 01 (Deposition) - 16 Nov 01 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Rossmann Methyltransferase, Protein Repair Isomerization, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Griffith, M. R. Sawaya, D. R. Boutz, N. Thapar, J. E. Katz, S. Clarke, T. O. Yeates
Crystal Structure Of A Protein Repair Methyltransferase Fro Pyrococcus Furiosus With Its L-Isoaspartyl Peptide Substrate.
J. Mol. Biol. V. 313 1103 2001
PubMed-ID: 11700066 | Reference-DOI: 10.1006/JMBI.2001.5095

Molecule 1 - PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.77
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261
	Synonym	:	PROTEIN-BETA-ASPARTATE METHYLTRANSFERASE

Molecule 2 - VYP(L-ISO-ASP)HA
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	HEXAPEPTIDE SUBSTRATE
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	ADN	2	Ligand/Ion	ADENOSINE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	IAS	2	Mod. Amino Acid	BETA-L-ASPARTIC ACID
4	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ADN	1	Ligand/Ion	ADENOSINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
4	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ADN	1	Ligand/Ion	ADENOSINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
4	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:146 , LEU A:194 , HOH A:1058	BINDING SITE FOR RESIDUE CL A 300
2	AC2	SOFTWARE	LEU B:146 , LEU B:194	BINDING SITE FOR RESIDUE CL B 301
3	AC3	SOFTWARE	THR B:73 , ADN B:550 , HOH B:1309 , HOH B:1336	BINDING SITE FOR RESIDUE NA B 401
4	AC4	SOFTWARE	THR A:73 , ADN A:500 , HOH A:1185 , HOH A:1307	BINDING SITE FOR RESIDUE NA A 402
5	AC5	SOFTWARE	GLN A:72 , THR A:73 , GLY A:99 , GLY A:101 , ILE A:120 , GLU A:121 , ARG A:122 , ILE A:123 , LEU A:126 , GLY A:147 , ASP A:148 , GLY A:149 , SER A:150 , THR A:165 , LEU A:221 , ILE A:222 , NA A:402 , HOH A:1042 , HOH A:1185	BINDING SITE FOR RESIDUE ADN A 500
6	AC6	SOFTWARE	GLN B:72 , THR B:73 , GLY B:99 , GLY B:101 , ILE B:120 , GLU B:121 , ARG B:122 , ILE B:123 , LEU B:126 , GLY B:147 , ASP B:148 , GLY B:149 , SER B:150 , THR B:165 , LEU B:221 , ILE B:222 , NA B:401 , HOH B:1082 , HOH B:1309 , HOH B:1336	BINDING SITE FOR RESIDUE ADN B 550

(no "SS Bond" information available for 1JG3)

Asymmetric Unit

No.	Residues
1	Ala A:157	-	Pro A:158
2	Ala B:157	-	Pro B:158

(no "SAP(SNP)/Variant" information available for 1JG3)

Asymmetric 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_PYRFU	137-152	2	A:147-162 B:147-162

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PCMT	PS01279	Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature.	PIMT_PYRFU	137-152	1	A:147-162 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PCMT	PS01279	Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature.	PIMT_PYRFU	137-152	1	- B:147-162

(no "Exon" information available for 1JG3)

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:215
 aligned with PIMT_PYRFU | Q8TZR3 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:215
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
           PIMT_PYRFU     4 EKELYEKWMRTVEMLKAEGIIRSKEVERAFLKYPRYLFVEDKYKKYAHIDEPLPIPAGQTVSAPHMVAIMLEIANLKPGMNILEVGTGSGWNAALISEIVKTDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPKAPYDVIIVTAGAPKIPEPLIEQLKIGGKLIIPVGSYHLWQELLEVRKTKDGIKIKNHGGVAFVPLIGEYGWK 218
               SCOP domains d1jg3a_ A: Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                                    SCOP domains
               CATH domains 1jg3A00 A:14-228 Vaccinia Virus protein VP39                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhheee.hhhhhhhhhhhhh......eeee....hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeee......eeeeeeee....eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------PCMT            ------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jg3 A  14 EKELYEKWMRTVEMLKAEGIIRSKEVERAFLKYPRYLSVEDKYKKYAHIDEPLPIPAGQTVSAPHMVAIMLEIANLKPGMNILEVGTGSGWNAALISEIVKTDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPKAPYDVIIVTAGAPKIPEPLIEQLKIGGKLIIPVGSYHLWQELLEVRKTKDGIKIKNHGGVAFVPLIGEYGWK 228
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with PIMT_PYRFU | Q8TZR3 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:215
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
           PIMT_PYRFU     4 EKELYEKWMRTVEMLKAEGIIRSKEVERAFLKYPRYLFVEDKYKKYAHIDEPLPIPAGQTVSAPHMVAIMLEIANLKPGMNILEVGTGSGWNAALISEIVKTDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPKAPYDVIIVTAGAPKIPEPLIEQLKIGGKLIIPVGSYHLWQELLEVRKTKDGIKIKNHGGVAFVPLIGEYGWK 218
               SCOP domains d1jg3b_ B: Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                                    SCOP domains
               CATH domains 1jg3B00 B:14-228 Vaccinia Virus protein VP39                                                                                                                                                                            CATH domains
           Pfam domains (1) -----PCMT-1jg3B01 B:19-226                                                                                                                                                                                           -- Pfam domains (1)
           Pfam domains (2) -----PCMT-1jg3B02 B:19-226                                                                                                                                                                                           -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eee.hhhhhhhhhhhhh......eeee....hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeee......eeeeeeeee..eeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------PCMT            ------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jg3 B  14 EKELYEKWMRTVEMLKAEGIIRSKEVERAFLKYPRYLSVEDKYKKYAHIDEPLPIPAGQTVSAPHMVAIMLEIANLKPGMNILEVGTGSGWNAALISEIVKTDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPKAPYDVIIVTAGAPKIPEPLIEQLKIGGKLIIPVGSYHLWQELLEVRKTKDGIKIKNHGGVAFVPLIGEYGWK 228
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1jg3 C   1 VYPxHA   6
                               |  
                               4-IAS

Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1jg3 D   1 VYPxHA   6
                               |  
                               4-IAS

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(

)

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)

Pyrococcus furiosus. Organism_taxid: 2261. (6)

1a	1jg3A00	A:14-228
1b	1jg3B00	B:14-228

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: PCMT (7)

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (4)

1a	PCMT-1jg3B01	B:19-226
1b	PCMT-1jg3B02	B:19-226

Asymmetric Unit(hide GO term definitions)

Chain A,B (PIMT_PYRFU | Q8TZR3)

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.

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	Cis Peptide Bonds
		Ala A:157 - Pro A:158	[ RasMol ]
		Ala B:157 - Pro B:158	[ RasMol ]

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	PIMT_PYRFU \| Q8TZR3	:	1jg1 1jg2 1jg4

(no "Related Entries Specified in the PDB File" available for 1JG3)

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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