1LZO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE-PHOSPHOGLYCOLATE COMPLEX

Authors :   S. Parthasarathy, H. Balaram, P. Balaram, M. R. Murthy

Date :   11 Jun 02 (Deposition) - 28 Jan 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Triosephosphate Isomerase; Phosphoglycolate; Loop Dynamics; Loop Open Conformation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Parthasarathy, G. Ravindra, H. Balaram, P. Balaram, M. R. Murthy
Structure Of The Plasmodium Falciparum Triosephosphate Isomerase-Phosphoglycolate Complex In Two Crystal Forms: Characterization Of Catalytic Loop Open And Closed Conformations In The Ligand-Bound State
Biochemistry V. 41 13178 2002
PubMed-ID: 12403619 | Reference-DOI: 10.1021/BI025783A
(for further references see the PDB file header)

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.3.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC 99A VECTOR, CALLED PARC
	Expression System Strain	:	AA200
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TPI
	Organism Common	:	MALARIA PARASITE P. FALCIPARUM
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	5833
	Synonym	:	TIM

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PGA	2	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PGA	1	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PGA	1	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:12 , SER B:211 , LEU B:230 , GLY B:232 , ASN B:233 , HOH B:580	BINDING SITE FOR RESIDUE PGA B 7251
2	AC2	SOFTWARE	LYS D:12 , GLY D:209 , SER D:211 , LEU D:230 , GLY D:232 , ASN D:233 , HOH D:645	BINDING SITE FOR RESIDUE PGA D 9251

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

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_PLAFA	4-246	4	A:4-246 B:4-246 C:4-246 D:4-246
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_PLAFA	163-173	4	A:164-173 B:164-173 C:164-173 D:164-173

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_PLAFA	4-246	2	A:4-246 B:4-246 - -
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_PLAFA	163-173	2	A:164-173 B:164-173 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_PLAFA	4-246	2	- - C:4-246 D:4-246
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_PLAFA	163-173	2	- - C:164-173 D:164-173

(no "Exon" information available for 1LZO)

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:246
 aligned with TPIS_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d1lzoa_ A: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1lzoA00 A:3-248 Aldolase class I                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhhh..eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhh..hhhhhhhhhhhhhhhhh.......eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhh.....eeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: A:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lzo A   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with TPIS_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d1lzob_ B: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1lzoB00 B:3-248 Aldolase class I                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhh......eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.hhhhh......hhhhhhhhhhhhhhhhhh..hhhhhh...eee.......hhhhhhh.....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: B:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lzo B   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain C from PDB  Type:PROTEIN  Length:246
 aligned with TPIS_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d1lzoc_ C: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1lzoC00 C:3-248 Aldolase class I                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhh....eeee...............hhhhhhhhh..eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhh..hhhhhhhhhhhhhhh.......eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhheee........hhhhhhh.....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: C:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lzo C   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain D from PDB  Type:PROTEIN  Length:246
 aligned with TPIS_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d1lzod_ D: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1lzoD00 D:3-248 Aldolase class I                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) --TIM-1lzoD01 D:5-244                                                                                                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) --TIM-1lzoD02 D:5-244                                                                                                                                                                                                                             ---- Pfam domains (2)
           Pfam domains (3) --TIM-1lzoD03 D:5-244                                                                                                                                                                                                                             ---- Pfam domains (3)
           Pfam domains (4) --TIM-1lzoD04 D:5-244                                                                                                                                                                                                                             ---- Pfam domains (4)
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhh....eeee...............hhhhhhh....eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh.......eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhh.....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: D:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lzo D   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

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: TIM beta/alpha-barrel (3956)

Superfamily: Triosephosphate isomerase (TIM) (148)

Family: Triosephosphate isomerase (TIM) (128)

Protein domain: Triosephosphate isomerase (126)

Malaria parasite (Plasmodium falciparum) [TaxId: 5833] (20)

1a	d1lzoa_	A:
1b	d1lzob_	B:
1c	d1lzoc_	C:
1d	d1lzod_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Malaria parasite p (Plasmodium falciparum) (13)

1a	1lzoA00	A:3-248
1b	1lzoB00	B:3-248
1c	1lzoC00	C:3-248
1d	1lzoD00	D:3-248

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: TIM (80)

Plasmodium falciparum (17)

1a	TIM-1lzoD01	D:5-244
1b	TIM-1lzoD02	D:5-244
1c	TIM-1lzoD03	D:5-244
1d	TIM-1lzoD04	D:5-244

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TPIS_PLAFA | Q07412)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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.

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1lyx	LOOP CLOSED FORM OF THE PFTIM-PHOSPHOGLYCOLATE COMPLEX
1ydv	UNBOUND STRUCTURE OF PFTIM

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