3LNT - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHOSPHOGLYCEROMUTASE FROM BURKHOLDERIA PSEUDOMALLEI 1710B WITH BOUND MALONIC ACID

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   03 Feb 10 (Deposition) - 09 Feb 10 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Mutase, Phosphoglycerylmutase, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Glycolysis, Isomerase (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, B
	EC Number	:	5.4.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	GPMA, BURPS1710B_0662
	Organism Scientific	:	BURKHOLDERIA PSEUDOMALLEI
	Organism Taxid	:	320372
	Strain	:	1710B
	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)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	MLI	2	Ligand/Ion	MALONATE ION
3	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	MLI	2	Ligand/Ion	MALONATE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MLI	1	Ligand/Ion	MALONATE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MLI	1	Ligand/Ion	MALONATE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:23 , HOH A:252 , HOH A:259 , HOH A:284	BINDING SITE FOR RESIDUE NA A 250
2	AC2	SOFTWARE	ARG A:8 , HIS A:9 , ASN A:15 , ARG A:19 , THR A:21 , GLY A:22 , GLU A:87 , TYR A:90 , HOH A:255 , HOH A:268 , HOH A:300 , HOH A:304 , HOH A:360	BINDING SITE FOR RESIDUE MLI A 990
3	AC3	SOFTWARE	ARG B:8 , HIS B:9 , ASN B:15 , ARG B:19 , THR B:21 , GLY B:22 , GLU B:87 , TYR B:90 , HOH B:273 , HOH B:322 , HOH B:327 , HOH B:359	BINDING SITE FOR RESIDUE MLI B 990
4	AC4	SOFTWARE	EDO A:251 , ARG B:63 , TRP B:66 , HIS B:67	BINDING SITE FOR RESIDUE EDO B 250
5	AC5	SOFTWARE	ARG A:63 , HIS A:67 , EDO B:250	BINDING SITE FOR RESIDUE EDO A 251
6	AC6	SOFTWARE	VAL A:79 , HOH A:260 , PRO B:78 , VAL B:79 , ARG B:115 , HOH B:289	BINDING SITE FOR RESIDUE EDO B 251

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

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

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

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	- B:6-15

(no "Exon" information available for 3LNT)

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:245
 aligned with GPMA_BURP1 | Q3JWH7 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:245
                             1                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
           GPMA_BURP1     - -MYKLVLIRHGESTWNKENRFTGWVDVDLTEQGNREARQAGQLLKEAGYTFDIAYTSVLKRAIRTLWHVQDQMDLMYVPVVHSWRLNERHYGALSGLNKAETAAKYGDEQVLVWRRSYDTPPPALEPGDERAPYADPRYAKVPREQLPLTECLKDTVARVLPLWNESIAPAVKAGKQVLIAAHGNSLRALIKYLDGISDADIVGLNIPNGVPLVYELDESLTPIRHYYLGDQEAIAKAQAAVAQQ 244
               SCOP domains d3lnta_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..................hhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh.....hhhhh.......eeeee.....eeeeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PG_MUTASE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lnt A   0 SMYKLVLIRHGESTWNKENRFTGWVDVDLTEQGNREARQAGQLLKEAGYTFDIAYTSVLKRAIRTLWHVQDQMDLMYVPVVHSWRLNERHYGALSGLNKAETAAKYGDEQVLVWRRSYDTPPPALEPGDERAPYADPRYAKVPREQLPLTECLKDTVARVLPLWNESIAPAVKAGKQVLIAAHGNSLRALIKYLDGISDADIVGLNIPNGVPLVYELDESLTPIRHYYLGDQEAIAKAQAAVAQQ 244
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

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 d3lntb_ B: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --His_Phos_1-3lntB01 B:3-189                                                                                                                                                                 ---------------------------------------- Pfam domains (1)
           Pfam domains (2) --His_Phos_1-3lntB02 B:3-189                                                                                                                                                                 ---------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..................hhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..hhhhhh.........eeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PG_MUTASE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lnt 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

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(

)

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: automated matches (41)

Burkholderia pseudomallei [TaxId: 320372] (3)

1a	d3lnta_	A:
1b	d3lntb_	B:

(no "CATH Domain" information available for 3LNT)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PGM (50)

Family: His_Phos_1 (31)

Burkholderia pseudomallei (strain 1710b) (1)

1a	His_Phos_1-3lntB01	B:3-189
1b	His_Phos_1-3lntB02	B:3-189

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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UniProtKB/Swiss-Prot
	GPMA_BURP1 \| Q3JWH7	:	3ezn 3fdz 3gp3 3gp5 3gw8

3ezn	CRYSTAL STRUCTURE OF PHOSPHOGLYCEROMUTASE FROM BURKHOLDERIA PSEUDOMALLEI 1710B RELATED ID: BUPSA.00114.A RELATED DB: TARGETDB
3fdz	CRYSTAL STRUCTURE OF PHOSPHOGLYCEROMUTASE FROM BURKHOLDERIA PSEUDOMALLEI 1710B WITH BOUND 2,3-DIPHOSPHOGLYCERIC ACID AND 3-PHOSPHOGLYCERIC ACID
3gp3	CRYSTAL STRUCTURE OF PHOSPHOGLYCEROMUTASE FROM BURKHOLDERIA PSEUDOMALLEI WITH 2-PHOSPHOSERINE
3gp5	CRYSTAL STRUCTURE OF PHOSPHOGLYCEROMUTASE FROM BURKHOLDERIA PSEUDOMALLEI WITH 3-PHOSPHOGLYCERIC ACID AND VANADATE
3gw8	CRYSTAL STRUCTURE OF PHOSPHOGLYCEROMUTASE FROM BURKHOLDERIA PSEUDOMALLEI WITH VANADATE AND GLYCEROL

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (8, 8)

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