1DL5 - JenaLib

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Title :   PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

Authors :   M. M. Skinner, J. M. Puvathingal, R. L. Walter, A. M. Friedman

Date :   08 Dec 99 (Deposition) - 08 Dec 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Methyltransferase, Isoaspartyl Residues, Protein Repair, Deamidation, Post-Translational Modification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. M. Skinner, J. M. Puvathingal, R. L. Walter, A. M. Friedman
Crystal Structure Of Protein Isoaspartyl Methyltransferase: A Catalyst For Protein Repair.
Structure Fold. Des. V. 8 1189 2000
PubMed-ID: 11080641 | Reference-DOI: 10.1016/S0969-2126(00)00522-0
(for further references see the PDB file header)

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	:	PET30B
	Expression System Taxid	:	562
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 21)

No.	Name	Count	Type	Full Name
1	CD	9	Ligand/Ion	CADMIUM ION
2	CL	10	Ligand/Ion	CHLORIDE ION
3	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CL A:603 , CL A:604 , HIS B:312	BINDING SITE FOR RESIDUE CD A 601
02	AC2	SOFTWARE	CD A:601 , CL A:604 , HIS B:312 , ILE B:313	BINDING SITE FOR RESIDUE CL A 603
03	AC3	SOFTWARE	CD A:601 , CL A:603 , GLN B:289 , HIS B:312 , ILE B:313	BINDING SITE FOR RESIDUE CL A 604
04	AC4	SOFTWARE	ASP A:271 , CL A:622 , CL A:623 , HOH A:842 , HIS B:238	BINDING SITE FOR RESIDUE CD A 621
05	AC5	SOFTWARE	ASP A:271 , CD A:621 , ARG B:236 , HIS B:238 , ILE B:239	BINDING SITE FOR RESIDUE CL A 622
06	AC6	SOFTWARE	ASP A:271 , ASP A:272 , CD A:621 , CD A:641 , HOH A:842 , HIS B:238	BINDING SITE FOR RESIDUE CL A 623
07	AC7	SOFTWARE	ASP A:272 , CL A:623 , HOH A:925 , HOH A:926	BINDING SITE FOR RESIDUE CD A 641
08	AC8	SOFTWARE	ASP A:16 , HOH B:1925	BINDING SITE FOR RESIDUE CD A 650
09	AC9	SOFTWARE	ASP B:74	BINDING SITE FOR RESIDUE CD A 651
10	BC1	SOFTWARE	GLU A:253 , GLU B:253 , CL B:702 , CL B:703	BINDING SITE FOR RESIDUE CD B 701
11	BC2	SOFTWARE	GLU A:253 , ASP B:255 , CD B:701	BINDING SITE FOR RESIDUE CL B 702
12	BC3	SOFTWARE	ASP A:255 , GLU B:253 , CD B:701	BINDING SITE FOR RESIDUE CL B 703
13	BC4	SOFTWARE	ASP A:279 , HOH A:930 , CL B:722 , CL B:723 , HOH B:1926	BINDING SITE FOR RESIDUE CD B 721
14	BC5	SOFTWARE	GLU A:284 , CD B:721 , CL B:723	BINDING SITE FOR RESIDUE CL B 722
15	BC6	SOFTWARE	ALA A:280 , GLU A:284 , CD B:721 , CL B:722	BINDING SITE FOR RESIDUE CL B 723
16	BC7	SOFTWARE	ASP B:279 , GLU B:284 , CL B:742 , CL B:743	BINDING SITE FOR RESIDUE CD B 741
17	BC8	SOFTWARE	TYR A:194 , ASN B:229 , ARG B:230 , ASP B:279 , CD B:741	BINDING SITE FOR RESIDUE CL B 742
18	BC9	SOFTWARE	ASN A:285 , CD B:741	BINDING SITE FOR RESIDUE CL B 743
19	CC1	SOFTWARE	ASP A:255 , GLU B:217 , HOH B:1766 , HOH B:1927 , HOH B:1928 , HOH B:1929	BINDING SITE FOR RESIDUE CD B 761
20	CC2	SOFTWARE	SER A:56 , THR A:57 , GLU A:81 , GLY A:83 , GLY A:84 , GLY A:85 , ASN A:89 , VAL A:106 , GLU A:107 , TYR A:108 , ASP A:134 , GLY A:135 , THR A:151 , VAL A:152 , ALA A:208 , GLY A:209 , LEU A:212 , HOH A:703 , HOH A:704 , HOH A:724 , HOH A:725 , HOH A:746 , HOH A:825	BINDING SITE FOR RESIDUE SAH A 699
21	CC3	SOFTWARE	SER B:56 , THR B:57 , GLU B:81 , GLY B:83 , GLY B:84 , GLY B:85 , ASN B:89 , VAL B:106 , GLU B:107 , TYR B:108 , ASP B:134 , GLY B:135 , THR B:151 , VAL B:152 , ALA B:208 , GLY B:209 , LEU B:212 , HOH B:1704 , HOH B:1708 , HOH B:1728 , HOH B:1740 , HOH B:1743 , HOH B:1761 , HOH B:1856	BINDING SITE FOR RESIDUE SAH B 1699

Asymmetric Unit

No.	Residues
1	A:113	-	A:132
2	A:293	-	A:315
3	B:113	-	B:132
4	B:293	-	B:315

Asymmetric Unit

No.	Residues
1	Ser A:143	-	Pro A:144
2	Asp A:192	-	Pro A:193
3	Ser B:143	-	Pro B:144
4	Asp B:192	-	Pro B:193

(no "SAP(SNP)/Variant" information available for 1DL5)

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_THEMA	133-148	2	A:133-148 B:133-148

Biological Unit 1 (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_THEMA	133-148	2	A:133-148 B:133-148

Biological Unit 2 (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_THEMA	133-148	2	A:133-148 B:133-148

(no "Exon" information available for 1DL5)

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:317
 aligned with PIMT_THEMA | Q56308 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:317
                                    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       260       270       280       290       300       310       
           PIMT_THEMA     1 MREKLFWILKKYGVSDHIAKAFLEIPREEFLTKSYPLSYVYEDIVLVSYDDGEEYSTSSQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEFSPYDVIFVTVGVDEVPETWFTQLKEGGRVIVPINLKLSRRQPAFLFKKKDPYLVGNYKLETRFITAGGNLGNLLERNRKLLREFPFNREILLVRSHIFVELVDLLTRRLTEIDGTFYYAGPNGVVEFLDDRMRIYGDAPEIENLLTQWESCGYRSFEYLMLHVGYNAFSHISCSI 317
               SCOP domains d1dl5a1 A:1-213 Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                            d1dl5a2 A:214-317 Protein-L-isoaspartyl O-methyltransferase, C-terminal domain                           SCOP domains
               CATH domains 1dl5A01 A:1-201 Vaccinia Virus protein VP39                                                                                                                                                              1dl5A02 A:202-317  [code=3.55.20.10, no name defined]                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhh....eeeee....eeee.hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeee...hhhh..eeeeeeee..eeeeeeeee......hhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhh.eeee..eeeee...eeeeee..eeeeee.hhhhhhhhhhhhhh...hhhhheeeee.....eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------PCMT            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dl5 A   1 MREKLFWILKKYGVSDHIAKAFLEIPREEFLTKSYPLSYVYEDIVLVSYDDGEEYSTSSQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEFSPYDVIFVTVGVDEVPETWFTQLKEGGRVIVPINLKLSRRQPAFLFKKKDPYLVGNYKLETRFITAGGNLGNLLERNRKLLREFPFNREILLVRSHIFVELVDLLTRRLTEIDGTFYYAGPNGVVEFLDDRMRIYGDAPEIENLLTQWESCGYRSFEYLMLHVGYNAFSHISCSI 317
                                    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       260       270       280       290       300       310

Chain B from PDB  Type:PROTEIN  Length:316
 aligned with PIMT_THEMA | Q56308 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:316
                                    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       260       270       280       290       300       310      
           PIMT_THEMA     1 MREKLFWILKKYGVSDHIAKAFLEIPREEFLTKSYPLSYVYEDIVLVSYDDGEEYSTSSQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEFSPYDVIFVTVGVDEVPETWFTQLKEGGRVIVPINLKLSRRQPAFLFKKKDPYLVGNYKLETRFITAGGNLGNLLERNRKLLREFPFNREILLVRSHIFVELVDLLTRRLTEIDGTFYYAGPNGVVEFLDDRMRIYGDAPEIENLLTQWESCGYRSFEYLMLHVGYNAFSHISCS 316
               SCOP domains d1dl5b1 B:1-213 Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                            d1dl5b2 B:214-316 Protein-L-isoaspartyl O-methyltransferase, C-terminal domain                          SCOP domains
               CATH domains 1dl5B01 B:1-201 Vaccinia Virus protein VP39                                                                                                                                                              1dl5B02 B:202-316  [code=3.55.20.10, no name defined]                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhh....eeeee....eeee.hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeee........eeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhh.eeee..eeeee...eeeee...eeeeee.hhhhhhhhhhhhhh...hhhhheeeee.....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------PCMT            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dl5 B   1 MREKLFWILKKYGVSDHIAKAFLEIPREEFLTKSYPLSYVYEDIVLVSYDDGEEYSTSSQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEFSPYDVIFVTVGVDEVPETWFTQLKEGGRVIVPINLKLSRRQPAFLFKKKDPYLVGNYKLETRFITAGGNLGNLLERNRKLLREFPFNREILLVRSHIFVELVDLLTRRLTEIDGTFYYAGPNGVVEFLDDRMRIYGDAPEIENLLTQWESCGYRSFEYLMLHVGYNAFSHISCS 316
                                    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       260       270       280       290       300       310

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

(no "Pfam Domain" information available for 1DL5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PIMT_THEMA | Q56308)

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 Unit
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	Cis Peptide Bonds
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		Asp B:192 - Pro B:193	[ RasMol ]
		Ser A:143 - Pro A:144	[ RasMol ]
		Ser B:143 - Pro B:144	[ RasMol ]

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Description

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