2OB2 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   PPM1 IN THE ABSENCE OF 1,8-ANS (CF 1JD)

Authors :   M. R. Groves, I. B. Mueller, X. Kreplin, J. Mueller-Dieckmann

Date :   18 Dec 06 (Deposition) - 30 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.92

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Ppm1 Without 1, 8-Ans (As 1Rjd), Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. R. Groves, I. B. Muller, X. Kreplin, J. Muller-Dieckmann
A Method For The General Identification Of Protein Crystals In Crystallization Experiments Using A Noncovalent Fluorescent Dye.
Acta Crystallogr. , Sect. D V. 63 526 2007
PubMed-ID: 17372358 | Reference-DOI: 10.1107/S0907444906056137

Molecule 1 - LEUCINE CARBOXYL METHYLTRANSFERASE 1
	Chains	:	A, B, C
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PETM11
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	PPM1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PROTEIN PHOSPHATASE METHYLTRANSFERASE 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	SAH	3	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
4	SMC	3	Mod. Amino Acid	S-METHYLCYSTEINE

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
4	SMC	1	Mod. Amino Acid	S-METHYLCYSTEINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	PO4	-1	Ligand/Ion	PHOSPHATE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
4	SMC	1	Mod. Amino Acid	S-METHYLCYSTEINE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	PO4	-1	Ligand/Ion	PHOSPHATE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
4	SMC	1	Mod. Amino Acid	S-METHYLCYSTEINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:300 , ARG A:303 , HOH A:2050 , HOH A:2164 , ARG C:303 , HOH C:1907	BINDING SITE FOR RESIDUE PO4 A 1001
2	AC2	SOFTWARE	ILE A:5 , GLN A:6 , THR A:8 , ASP A:9 , ALA A:12 , ARG A:81 , GLY A:105 , CYS A:106 , GLY A:107 , ASP A:128 , TYR A:129 , CYS A:174 , ASP A:175 , LEU A:176 , ASN A:177 , GLU A:201 , SMC A:202 , LEU A:203 , HOH A:2038 , HOH A:2115 , HOH A:2145 , HOH A:2205 , HOH A:2209	BINDING SITE FOR RESIDUE SAH A 1801
3	AC3	SOFTWARE	ILE B:5 , GLN B:6 , THR B:8 , ASP B:9 , ALA B:12 , ARG B:81 , GLY B:105 , CYS B:106 , GLY B:107 , ASP B:128 , TYR B:129 , CYS B:174 , ASP B:175 , LEU B:176 , ASN B:177 , GLU B:201 , SMC B:202 , LEU B:203 , HOH B:1806 , HOH B:1837 , HOH B:1948 , HOH B:1965 , HOH B:1992 , HOH B:1993	BINDING SITE FOR RESIDUE SAH B 1802
4	AC4	SOFTWARE	ILE C:5 , GLN C:6 , THR C:8 , ASP C:9 , ALA C:12 , ARG C:81 , GLY C:105 , CYS C:106 , GLY C:107 , ASP C:128 , TYR C:129 , CYS C:174 , ASP C:175 , LEU C:176 , ASN C:177 , GLU C:201 , SMC C:202 , LEU C:203 , TYR C:206 , HOH C:1870 , HOH C:1921 , HOH C:1928	BINDING SITE FOR RESIDUE SAH C 1803
5	AC5	SOFTWARE	GLY A:77 , THR A:78 , ARG A:81 , TYR A:231 , MET A:317 , GLN A:318 , TYR A:321	BINDING SITE FOR RESIDUE GOL A 2002
6	AC6	SOFTWARE	ARG A:32 , SER A:34 , HOH A:2066 , HOH A:2076 , HOH A:2079 , ARG B:32 , MET B:118 , PHE B:119 , HOH B:1960	BINDING SITE FOR RESIDUE GOL A 2003

(no "SS Bond" information available for 2OB2)

Asymmetric Unit

No.	Residues
1	Leu A:25	-	Pro A:26
2	Ser A:160	-	Pro A:161
3	Leu B:25	-	Pro B:26
4	Ser B:160	-	Pro B:161
5	Leu C:25	-	Pro C:26
6	Ser C:160	-	Pro C:161

(no "SAP(SNP)/Variant" information available for 2OB2)

(no "PROSITE Motif" information available for 2OB2)

Asymmetric Unit (1, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR435C	1	YDR435C.1	IV:1333962-1332976	987	LCMT1_YEAST	1-328	328	3	A:2-328 B:2-328 C:2-328	327 327 327

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:327
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:327
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       
          LCMT1_YEAST     2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
               SCOP domains d2ob2a_ A: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2ob2A00 A:2-328 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhh............eeeee..eeeee....hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhh...........hhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh.eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                      Transcript 1
                 2ob2 A   2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISEcLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|      211       221       231       241       251       261       271       281       291       301       311       321       
                                                                                                                                                                                                                                  202-SMC

Chain B from PDB  Type:PROTEIN  Length:327
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:327
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       
          LCMT1_YEAST     2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
               SCOP domains d2ob2b_ B: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2ob2B00 B:2-328 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhh............hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                      Transcript 1
                 2ob2 B   2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISEcLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|      211       221       231       241       251       261       271       281       291       301       311       321       
                                                                                                                                                                                                                                  202-SMC

Chain C from PDB  Type:PROTEIN  Length:327
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:327
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       
          LCMT1_YEAST     2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
               SCOP domains d2ob2c_ C: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2ob2C00 C:2-328 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ----------------------LCM-2ob2C01 C:24-220                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------LCM-2ob2C02 C:24-220                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) ----------------------LCM-2ob2C03 C:24-220                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------ Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhh............hhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh.eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:2-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                      Transcript 1
                 2ob2 C   2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISEcLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|      211       221       231       241       251       261       271       281       291       301       311       321       
                                                                                                                                                                                                                                  202-SMC

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)

Baker's yeast (Saccharomyces cerevisiae) (8)

1a	2ob2A00	A:2-328
1b	2ob2B00	B:2-328
1c	2ob2C00	C:2-328

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: LCM (10)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (6)

1a	LCM-2ob2C01	C:24-220
1b	LCM-2ob2C02	C:24-220
1c	LCM-2ob2C03	C:24-220

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (LCMT1_YEAST | Q04081)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0018423	protein C-terminal leucine carboxyl O-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + protein L-leucine = S-adenosyl-L-homocysteine + protein L-leucine methyl ester. This modification occurs only at the oxygen atoms of the free alpha carboxyl group of a leucine residue at the C-terminus of the protein.
	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:0006481	C-terminal protein methylation	The methylation of the C-terminal amino acid of a protein.
	GO:0043623	cellular protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0010506	regulation of autophagy	Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
		Leu A:25 - Pro A:26	[ RasMol ]
		Leu B:25 - Pro B:26	[ RasMol ]
		Leu C:25 - Pro C:26	[ RasMol ]
		Ser A:160 - Pro A:161	[ RasMol ]
		Ser B:160 - Pro B:161	[ RasMol ]
		Ser C:160 - Pro C:161	[ RasMol ]

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	2ob2
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	2.1.1.-
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	LCMT1_YEAST \| Q04081	:	1rjd 1rje 1rjf 1rjg 2ob1

2ob1	PPM1 WITH 1,8-ANS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 3)

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Related Entries

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Related Entries Specified in the PDB File