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Title :   CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS AT 1.9 ANGSTROM RESOLUTION

Authors :   S. Mukherjee, D. Dutta, B. Saha, A. K. Das

Date :   23 Mar 10 (Deposition) - 06 Apr 11 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Tim Barrel, Glycolysis, Gluconeogenesis, Isomerase, Pentose Shunt (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Mukherjee, A. Roychowdhury, D. Dutta, A. K. Das
Crystal Structures Of Triosephosphate Isomerase From Methicillin Resistant Staphylococcus Aureus Mrsa252 Provide Structural Insights Into Novel Modes Of Ligand Binding And Unique Conformations Of Catalytic Loop
Biochimie V. 94 2532 2012
PubMed-ID: 22813930 | Reference-DOI: 10.1016/J.BIOCHI.2012.07.001

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SAR0830, TPI, TPIA
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	282458
	Strain	:	MRSA252
	Synonym	:	TIM, TRIOSE-PHOSPHATE ISOMERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET B:225 , GLN B:227 , ILE B:230 , HOH B:305 , HOH B:327 , HOH B:359	BINDING SITE FOR RESIDUE NA B 254
2	AC2	SOFTWARE	THR A:80 , PRO B:42 , ALA B:43 , ILE B:44	BINDING SITE FOR RESIDUE NA B 255
3	AC3	SOFTWARE	LYS B:11 , SER B:215 , LYS B:217 , GLY B:236 , GLY B:237 , HOH B:285 , HOH B:301 , HOH B:306 , HOH B:354 , HOH B:355 , HOH B:365 , HOH B:475	BINDING SITE FOR RESIDUE CIT B 256

(no "SS Bond" information available for 3M9Y)

(no "Cis Peptide Bond" information available for 3M9Y)

(no "SAP(SNP)/Variant" information available for 3M9Y)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_STAAR	3-251	2	A:3-251 B:3-251
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_STAAR	167-177	2	A:167-175 B:167-177

(no "Exon" information available for 3M9Y)

Asymmetric/Biological 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:252
 aligned with TPIS_STAAR | Q6GIL6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:254
                             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       249    
           TPIS_STAAR     - -MRTPIIAGNWKMNKTVQEAKDFVNALPTLPDSKEVESVICAPAIQLDALTTAVKEGKAQGLEIGAQNTYFEDNGAFTGETSPVALADLGVKYVVIGHSERRELFHETDEEINKKAHAIFKHGMTPIICVGETDEERESGKANDVVGEQVKKAVAGLSEDQLKSVVIAYEPIWAIGTGKSSTSEDANEMCAFVRQTIADLSSKEVSEATRIQYGGSVKPNNIKEYMAQTDIDGALVGGASLKVEDFVQLLEGAK 253
               SCOP domains d3m9ya_ A: Triosephosphate isomerase                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhh.........eeeeeehhhhhhhhhhhhhh......eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhheeee.hhhhh.--...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhh.....eeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TIM_2  PDB: A:3-251 UniProt: 3-251                                                                                                                                                                                                                       -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      ---------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m9y A   0 SMRTPIIAGNWKMNKTVQEAKDFVNALPTLPDSKEVESVICAPAIQLDALTTAVKEGKAQGLEIGAQNTYFEDNGAFTGETSPVALADLGVKYVVIGHSERRELFHETDEEINKKAHAIFKHGMTPIICVGETDEERESGKANDVVGEQVKKAVAGLSEDQLKSVVIAYEPIWAIG--KSSTSEDANEMCAFVRQTIADLSSKEVSEATRIQYGGSVKPNNIKEYMAQTDIDGALVGGASLKVEDFVQLLEGAK 253
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169     | 179       189       199       209       219       229       239       249    
                                                                                                                                                                                                         175  |                                                                           
                                                                                                                                                                                                            178

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with TPIS_STAAR | Q6GIL6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:254
                             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       249    
           TPIS_STAAR     - -MRTPIIAGNWKMNKTVQEAKDFVNALPTLPDSKEVESVICAPAIQLDALTTAVKEGKAQGLEIGAQNTYFEDNGAFTGETSPVALADLGVKYVVIGHSERRELFHETDEEINKKAHAIFKHGMTPIICVGETDEERESGKANDVVGEQVKKAVAGLSEDQLKSVVIAYEPIWAIGTGKSSTSEDANEMCAFVRQTIADLSSKEVSEATRIQYGGSVKPNNIKEYMAQTDIDGALVGGASLKVEDFVQLLEGAK 253
               SCOP domains d3m9yb_ B: Triosephosphate isomerase                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----TIM-3m9yB01 B:4-249                                                                                                                                                                                                                                   ---- Pfam domains (1)
           Pfam domains (2) ----TIM-3m9yB02 B:4-249                                                                                                                                                                                                                                   ---- Pfam domains (2)
         Sec.struct. author .....eeeee.....hhhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhh......eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhh...hhhhhhhheeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhh.....eeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TIM_2  PDB: B:3-251 UniProt: 3-251                                                                                                                                                                                                                       -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      ---------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m9y B   0 SMRTPIIAGNWKMNKTVQEAKDFVNALPTLPDSKEVESVICAPAIQLDALTTAVKEGKAQGLEIGAQNTYFEDNGAFTGETSPVALADLGVKYVVIGHSERRELFHETDEEINKKAHAIFKHGMTPIICVGETDEERESGKANDVVGEQVKKAVAGLSEDQLKSVVIAYEPIWAIGTGKSSTSEDANEMCAFVRQTIADLSSKEVSEATRIQYGGSVKPNNIKEYMAQTDIDGALVGGASLKVEDFVQLLEGAK 253
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

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: TIM beta/alpha-barrel (3956)

Superfamily: Triosephosphate isomerase (TIM) (148)

Family: Triosephosphate isomerase (TIM) (128)

Protein domain: Triosephosphate isomerase (126)

Staphylococcus aureus [TaxId: 282458] (6)

1a	d3m9ya_	A:
1b	d3m9yb_	B:

(no "CATH Domain" information available for 3M9Y)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: TIM (80)

Staphylococcus aureus (strain MRSA252) (1)

1a	TIM-3m9yB01	B:4-249
1b	TIM-3m9yB02	B:4-249

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TPIS_STAAR | Q6GIL6)

molecular function
	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: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:0004807	triose-phosphate isomerase activity	Catalysis of the reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate.
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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0006098	pentose-phosphate shunt	The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	TPIS_STAAR \| Q6GIL6	:	3uwu 3uwv 3uww 3uwy 3uwz

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