3PSV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF E97D MUTANT OF TIM FROM PLASMODIUM FALCIPARUM

Authors :   M. Samanta, M. R. N. Murthy, H. Balaram, P. Balaram

Date :   02 Dec 10 (Deposition) - 19 Oct 11 (Release) - 19 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   M. Samanta, M. R. N. Murthy, H. Balaram, P. Balaram
Revisiting The Mechanism Of The Triosephosphate Isomerase Reaction: The Role Of The Fully Conserved Glutamic Acid 97 Residue
Chembiochem V. 12 1886 2011
PubMed-ID: 21671330 | Reference-DOI: 10.1002/CBIC.201100116

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99A
	Expression System Strain	:	AA200
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TPI
	Mutation	:	YES
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	5833
	Synonym	:	TIM, TRIOSE-PHOSPHATE ISOMERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:211 , GLY A:232 , ASN A:233 , EDO A:250 , HOH A:306 , HOH A:428 , HOH A:431	BINDING SITE FOR RESIDUE SO4 A 249
2	AC2	SOFTWARE	ASN A:10 , LYS A:12 , HIS A:95 , LEU A:230 , GLY A:232 , SO4 A:249 , HOH A:284 , HOH A:287	BINDING SITE FOR RESIDUE EDO A 250
3	AC3	SOFTWARE	LYS B:12 , GLY B:232 , ASN B:233 , EDO B:250 , HOH B:340 , HOH B:458	BINDING SITE FOR RESIDUE SO4 B 249
4	AC4	SOFTWARE	ASN B:10 , LYS B:12 , HIS B:95 , GLY B:209 , LEU B:230 , VAL B:231 , GLY B:232 , SO4 B:249 , HOH B:261 , HOH B:275	BINDING SITE FOR RESIDUE EDO B 250
5	AC5	SOFTWARE	CYS A:196 , ARG B:52 , LYS B:53 , LEU B:55	BINDING SITE FOR RESIDUE SO4 B 251

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

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

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

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_PLAFA	4-246	2	A:4-246 B:4-246
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_PLAFA	163-173	2	A:164-171 B:164-173

(no "Exon" information available for 3PSV)

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:243
 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 d3psva_ A: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.hhhhh.---..hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......hhhhhhh.....eeeehhhhhhhhhhhhhhh.. 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
                 3psv A   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFDRRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIG---TATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        |-  |    182       192       202       212       222       232       242      
                                                                                                                                                                                                  171 175

Chain B from PDB  Type:PROTEIN  Length:244
 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 d3psvb_ B: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.....--.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.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
                 3psv B   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFDRRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWA--TGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 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      
                                                                                                                                                                                                169  |                                                                            
                                                                                                                                                                                                   172

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)

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

1a	d3psva_	A:
1b	d3psvb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3psv)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3psv
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TPIS_PLAFA \| Q07412
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	5.3.1.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TPIS_PLAFA \| Q07412
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File