3FDZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHOSPHOGLYCEROMUTASE FROM BURKHOLDERIA PSEUDOMALLEI 1710B WITH BOUND 2,3-DIPHOSPHOGLYCERIC ACID AND 3-PHOSPHOGLYCERIC ACID

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   26 Nov 08 (Deposition) - 13 Jan 09 (Release) - 20 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Isomerase, Ssgcid, Phosphoglyceromutase, Burkholderia Pseudomallei, Glycolysis, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. R. Davies, B. L. Staker, J. A. Abendroth, T. E. Edwards, R. Hartley, J. Leonard, H. Kim, A. L. Rychel, S. N. Hewitt, P. J. Myler, L. J. Stewart
An Ensemble Of Structures Of Burkholderia Pseudomallei 2, 3-Bisphosphoglycerate-Dependent Phosphoglycerate Mutase.
Acta Crystallogr. , Sect. F V. 67 1044 2011
PubMed-ID: 21904048 | Reference-DOI: 10.1107/S1744309111030405

Molecule 1 - 2,3-BISPHOSPHOGLYCERATE-DEPENDENT PHOSPHOGLYCERATE MUTASE
	Chains	:	A
	EC Number	:	5.4.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BURPS1710B_0662, GPMA
	Organism Scientific	:	BURKHOLDERIA PSEUDOMALLEI 1710B
	Organism Taxid	:	320372
	Strain	:	1719B
	Synonym	:	PHOSPHOGLYCEROMUTASE, PGAM, BPG-DEPENDENT PGAM, DPGM

Molecule 2 - 2,3-BISPHOSPHOGLYCERATE-DEPENDENT PHOSPHOGLYCERATE MUTASE
	Chains	:	B
	EC Number	:	5.4.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BURPS1710B_0662, GPMA
	Organism Scientific	:	BURKHOLDERIA PSEUDOMALLEI 1710B
	Organism Taxid	:	320372
	Strain	:	1719B
	Synonym	:	PHOSPHOGLYCEROMUTASE, PGAM, BPG-DEPENDENT PGAM, DPGM

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	3PG	1	Ligand/Ion	3-PHOSPHOGLYCERIC ACID
2	DG2	1	Ligand/Ion	(2R)-2,3-DIPHOSPHOGLYCERIC ACID
3	NEP	1	Mod. Amino Acid	N1-PHOSPHONOHISTIDINE
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	3PG	1	Ligand/Ion	3-PHOSPHOGLYCERIC ACID
2	DG2	1	Ligand/Ion	(2R)-2,3-DIPHOSPHOGLYCERIC ACID
3	NEP	1	Mod. Amino Acid	N1-PHOSPHONOHISTIDINE
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	3PG	-1	Ligand/Ion	3-PHOSPHOGLYCERIC ACID
2	DG2	1	Ligand/Ion	(2R)-2,3-DIPHOSPHOGLYCERIC ACID
3	NEP	-1	Mod. Amino Acid	N1-PHOSPHONOHISTIDINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	3PG	-1	Ligand/Ion	3-PHOSPHOGLYCERIC ACID
2	DG2	1	Ligand/Ion	(2R)-2,3-DIPHOSPHOGLYCERIC ACID
3	NEP	-1	Mod. Amino Acid	N1-PHOSPHONOHISTIDINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:8 , HIS A:9 , ASN A:15 , THR A:21 , GLY A:22 , ARG A:60 , GLU A:87 , TYR A:90 , LYS A:98 , ARG A:114 , ARG A:115 , HIS A:182 , GLY A:183 , ASN A:184 , HOH A:349 , HOH A:350 , HOH A:355	BINDING SITE FOR RESIDUE DG2 A1001
2	AC2	SOFTWARE	ASP A:194 , LEU A:204 , TYR A:214 , HIS A:225 , TYR A:227 , HOH A:259	BINDING SITE FOR RESIDUE PEG A1002
3	AC3	SOFTWARE	NEP B:9 , ARG B:19 , PHE B:20 , THR B:21 , GLY B:22 , GLU B:87 , TYR B:90 , LYS B:98 , ARG B:114 , ARG B:115 , ASN B:184 , HOH B:330	BINDING SITE FOR RESIDUE 3PG B1001
4	AC4	SOFTWARE	ILE B:190 , LEU B:204 , TYR B:214 , HIS B:225 , TYR B:227 , HOH B:366	BINDING SITE FOR RESIDUE PEG B1002

(no "SS Bond" information available for 3FDZ)

(no "Cis Peptide Bond" information available for 3FDZ)

(no "SAP(SNP)/Variant" information available for 3FDZ)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PG_MUTASE	PS00175	Phosphoglycerate mutase family phosphohistidine signature.	GPMA_BURP1	6-15	2	A:6-15 B:6-15

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PG_MUTASE	PS00175	Phosphoglycerate mutase family phosphohistidine signature.	GPMA_BURP1	6-15	2	A:6-15 B:6-15

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PG_MUTASE	PS00175	Phosphoglycerate mutase family phosphohistidine signature.	GPMA_BURP1	6-15	1	A:6-15 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PG_MUTASE	PS00175	Phosphoglycerate mutase family phosphohistidine signature.	GPMA_BURP1	6-15	1	A:6-15 -

(no "Exon" information available for 3FDZ)

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:230
 aligned with GPMA_BURP1 | Q3JWH7 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           GPMA_BURP1     1 MYKLVLIRHGESTWNKENRFTGWVDVDLTEQGNREARQAGQLLKEAGYTFDIAYTSVLKRAIRTLWHVQDQMDLMYVPVVHSWRLNERHYGALSGLNKAETAAKYGDEQVLVWRRSYDTPPPALEPGDERAPYADPRYAKVPREQLPLTECLKDTVARVLPLWNESIAPAVKAGKQVLIAAHGNSLRALIKYLDGISDADIVGLNIPNGVPLVYELDESLTPIRHYYLGD 230
               SCOP domains d3fdza_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 3fdzA00 A:1-230 Phosphoglycerate mutase-like                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..................hhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.hhhhhh.........eeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PG_MUTASE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdz A   1 MYKLVLIRHGESTWNKENRFTGWVDVDLTEQGNREARQAGQLLKEAGYTFDIAYTSVLKRAIRTLWHVQDQMDLMYVPVVHSWRLNERHYGALSGLNKAETAAKYGDEQVLVWRRSYDTPPPALEPGDERAPYADPRYAKVPREQLPLTECLKDTVARVLPLWNESIAPAVKAGKQVLIAAHGNSLRALIKYLDGISDADIVGLNIPNGVPLVYELDESLTPIRHYYLGD 230
                                    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:229
 aligned with GPMA_BURP1 | Q3JWH7 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
           GPMA_BURP1     1 MYKLVLIRHGESTWNKENRFTGWVDVDLTEQGNREARQAGQLLKEAGYTFDIAYTSVLKRAIRTLWHVQDQMDLMYVPVVHSWRLNERHYGALSGLNKAETAAKYGDEQVLVWRRSYDTPPPALEPGDERAPYADPRYAKVPREQLPLTECLKDTVARVLPLWNESIAPAVKAGKQVLIAAHGNSLRALIKYLDGISDADIVGLNIPNGVPLVYELDESLTPIRHYYLG 229
               SCOP domains d3fdzb_ B: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains 3fdzB00 B:1-229 Phosphoglycerate mutase-like                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..................hhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh................eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PG_MUTASE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdz B   1 MYKLVLIRhGESTWNKENRFTGWVDVDLTEQGNREARQAGQLLKEAGYTFDIAYTSVLKRAIRTLWHVQDQMDLMYVPVVHSWRLNERHYGALSGLNKAETAAKYGDEQVLVWRRSYDTPPPALEPGDERAPYADPRYAKVPREQLPLTECLKDTVARVLPLWNESIAPAVKAGKQVLIAAHGNSLRALIKYLDGISDADIVGLNIPNGVPLVYELDESLTPIRHYYLG 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
                                    9-NEP

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Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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: automated matches (41)

Burkholderia pseudomallei [TaxId: 320372] (3)

1a	d3fdza_	A:
1b	d3fdzb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Phosphoglycerate mutase-like (91)

Burkholderia pseudomallei 1710b. Organism_taxid: 320372. Strain: 1719b. (2)

1a	3fdzA00	A:1-230
1b	3fdzB00	B:1-229

(no "Pfam Domain" information available for 3FDZ)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GPMA_BURP1 | Q3JWH7)

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.

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	3fdz
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	GPMA_BURP1 \| Q3JWH7	:	3ezn 3gp3 3gp5 3gw8 3lnt

3ezn	SAME STRUCTURE WITHOUT LIGANDS RELATED ID: BUPSA.00114.A RELATED DB: TARGETDB
3gp3
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