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Asym./Biol. Unit (Jmol Viewer)

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Title :   SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH BENZENE HEXACARBOXYLATE

Authors :   D. J. Rigden, S. E. V. Phillips, L. A. Fothergill-Gilmore

Date :   20 Aug 98 (Deposition) - 26 Aug 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Isomerase, Transferase (Phosphoryl), Glycolytic Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Rigden, R. A. Walter, S. E. Phillips, L. A. Fothergill-Gilmore
Polyanionic Inhibitors Of Phosphoglycerate Mutase: Combined Structural And Biochemical Analysis.
J. Mol. Biol. V. 289 691 1999
PubMed-ID: 10369755 | Reference-DOI: 10.1006/JMBI.1999.2848
(for further references see the PDB file header)

Molecule 1 - PROTEIN (PHOSPHOGLYCERATE MUTASE 1)
	Cellular Location	:	CYTOPLASM
	Chains	:	D, C, A, B
	EC Number	:	5.4.2.1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PHOSPHOGLYCEROMUTASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BHC	1	Ligand/Ion	BENZENE HEXACARBOXYLIC ACID
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS D:8 , SER D:11 , ASN D:14 , THR D:20 , ARG D:59	BINDING SITE FOR RESIDUE SO4 D 300
2	AC2	SOFTWARE	SER C:11 , ASN C:14 , THR C:20 , ARG C:59	BINDING SITE FOR RESIDUE SO4 C 301
3	AC3	SOFTWARE	HIS B:8 , SER B:11 , ASN B:14 , THR B:20 , ARG B:59	BINDING SITE FOR RESIDUE SO4 B 303
4	AC4	SOFTWARE	ARG A:7 , ASN A:14 , TYR A:89 , LYS A:97 , ARG A:113 , ARG A:114 , ASN A:183 , ASN A:204	BINDING SITE FOR RESIDUE BHC A 302
5	CAA	AUTHOR	HIS A:8 , HIS A:181 , ARG A:7 , GLU A:86	CATALYTIC SITE. HIS 8 PHOSPHORYLATION IS REQUIRED TO PRIME THE ENZYME.
6	CAB	AUTHOR	HIS B:8 , HIS B:181 , ARG B:7 , GLU B:86	CATALYTIC SITE. HIS 8 PHOSPHORYLATION IS REQUIRED TO PRIME THE ENZYME.
7	CAC	AUTHOR	HIS C:8 , HIS C:181 , ARG C:7 , GLU C:86	CATALYTIC SITE. HIS 8 PHOSPHORYLATION IS REQUIRED TO PRIME THE ENZYME.
8	CAD	AUTHOR	HIS D:8 , HIS D:181 , ARG D:7 , GLU D:86	CATALYTIC SITE. HIS 8 PHOSPHORYLATION IS REQUIRED TO PRIME THE ENZYME.

(no "SS Bond" information available for 1BQ4)

(no "Cis Peptide Bond" information available for 1BQ4)

(no "SAP(SNP)/Variant" information available for 1BQ4)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PG_MUTASE	PS00175	Phosphoglycerate mutase family phosphohistidine signature.	PMG1_YEAST	6-15	4	A:5-14 B:5-14 C:5-14 D:5-14

Asymmetric/Biological Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YKL152C	1	YKL152C.1	XI:164390-163647	744	PMG1_YEAST	1-247	247	4	A:1-234 B:1-235 C:1-235 D:1-234	234 235 235 234

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:234
 aligned with PMG1_YEAST | P00950 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           PMG1_YEAST     2 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAA 235
               SCOP domains d1bq4a_ A: Phosphoglycerate mutase                                                                                                                                                                                                         SCOP domains
               CATH domains 1bq4A00 A:1-234 Phosphoglycerate mutase-like                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....................hhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhh......eeee.hhh.....hhh....hhhhhhhhhhhhhhhhhh....................hhh....hhh......hhhhhhhhhhhhhh.hhhhhhh..eeeeee.hhhhhhhhhhhh................eeeee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PG_MUTASE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-234 UniProt: 1-247 [INCOMPLETE]                                                                                                                                                                                         Transcript 1
                 1bq4 A   1 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAA 234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with PMG1_YEAST | P00950 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:235
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
           PMG1_YEAST     2 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAA 236
               SCOP domains d1bq4b_ B: Phosphoglycerate mutase                                                                                                                                                                                                          SCOP domains
               CATH domains 1bq4B00 B:1-235 Phosphoglycerate mutase-like                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhh..............hhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhh.....eeee.hhh.....hhh....hhhhhhhhhhhhhhhhhh....................hhh....hhh......hhhhhhhhhhhhhh.hhhhhh...eeeeee.hhhhhhhhhhhh......hhh........eeee...............hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PG_MUTASE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-235 UniProt: 1-247 [INCOMPLETE]                                                                                                                                                                                          Transcript 1
                 1bq4 B   1 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAA 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain C from PDB  Type:PROTEIN  Length:235
 aligned with PMG1_YEAST | P00950 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:235
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
           PMG1_YEAST     2 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAA 236
               SCOP domains d1bq4c_ C: Phosphoglycerate mutase                                                                                                                                                                                                          SCOP domains
               CATH domains 1bq4C00 C:1-235 Phosphoglycerate mutase-like                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhh.............hhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhh.....eeee.hhh.....hhh....hhhhhh...hhhhhhhhh....................hhh.............hhhhhhhhhhhhhh.hhhhhhh..eeeeee.hhhhhhhhhhh....hhhhhh.......eeeee...............hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PG_MUTASE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-235 UniProt: 1-247 [INCOMPLETE]                                                                                                                                                                                          Transcript 1
                 1bq4 C   1 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAA 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain D from PDB  Type:PROTEIN  Length:234
 aligned with PMG1_YEAST | P00950 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           PMG1_YEAST     2 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAA 235
               SCOP domains d1bq4d_ D: Phosphoglycerate mutase                                                                                                                                                                                                         SCOP domains
               CATH domains 1bq4D00 D:1-234 Phosphoglycerate mutase-like                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhh..............hhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhh.....eeee.hhh.....hhh....hhhhhhhh.hhhhhhhhh....................hhh....hhh......hhhhhhhhhhhhhh.hhhhhhh..eeeee..hhhhhhhhhhhh......hhh.......eeeee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PG_MUTASE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:1-234 UniProt: 1-247 [INCOMPLETE]                                                                                                                                                                                         Transcript 1
                 1bq4 D   1 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAA 234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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: Phosphoglycerate mutase-like (103)

Superfamily: Phosphoglycerate mutase-like (103)

Family: Cofactor-dependent phosphoglycerate mutase (57)

Protein domain: Phosphoglycerate mutase (12)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (6)

1a	d1bq4a_	A:
1b	d1bq4b_	B:
1c	d1bq4c_	C:
1d	d1bq4d_	D:

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: Phosphoglycerate mutase-like (91)

Baker's yeast (Saccharomyces cerevisiae) (6)

1a	1bq4A00	A:1-234
1b	1bq4D00	D:1-234
1c	1bq4B00	B:1-235
1d	1bq4C00	C:1-235

(no "Pfam Domain" information available for 1BQ4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (PMG1_YEAST | P00950)

molecular function
	GO:0046538	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity	Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate; this reaction requires the cofactor 2,3-bisphosphoglycerate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016868	intramolecular transferase activity, phosphotransferases	Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0004619	phosphoglycerate mutase activity	Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate.
biological process
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0043456	regulation of pentose-phosphate shunt	Any process that modulates the frequency, rate or extent of the pentose-phosphate shunt, the process in which glucose is oxidized, coupled to NADPH synthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	1bq4
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(no "Related Entries Specified in the PDB File" available for 1BQ4)

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (8, 8)

SS Bonds (0, 0)

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