2DP3 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A DOUBLE MUTANT (C202A/A198V) OF TRIOSEPHOSPHATE ISOMERASE FROM GIARDIA LAMBLIA

Authors :   A. Diaz, H. Reyes-Vivas, G. Lopez-Velazquez

Date :   05 May 06 (Deposition) - 02 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Triosephosphate Isomerase, Giardia, Enzyme, Alpha/Beta Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Reyes-Vivas, A. Diaz, J. Peon, G. Mendoza-Hernandez, G. Hernandez-Alcantara, I. De La Mora-De La Mora, S. Enriquez-Flores, L. Dominguez-Ramirez, G. Lopez-Velazquez
Disulfide Bridges In The Mesophilic Triosephosphate Isomerase From Giardia Lamblia Are Related To Oligomerization And Activity
J. Mol. Biol. V. 365 752 2007
PubMed-ID: 17095008 | Reference-DOI: 10.1016/J.JMB.2006.10.053
(for further references see the PDB file header)

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
	Chains	:	A
	EC Number	:	5.3.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)PLYS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLTIM
	Mutation	:	YES
	Organism Scientific	:	GIARDIA INTESTINALIS
	Organism Taxid	:	5741
	Strain	:	WB STRAIN
	Synonym	:	TIM, TRIOSE-PHOSPHATE ISOMERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:174 , ILE A:175 , GLY A:176 , SER A:216 , GLY A:237 , GLY A:238 , HOH A:923 , HOH A:925 , HOH A:943 , HOH A:1001	BINDING SITE FOR RESIDUE SO4 A 900
2	AC2	SOFTWARE	ARG A:135 , GLN A:185 , HOH A:1084	BINDING SITE FOR RESIDUE SO4 A 901
3	AC3	SOFTWARE	LYS A:195 , ASN A:218 , ALA A:239 , LYS A:242 , GLU A:244 , HOH A:1136 , HOH A:1137 , HOH A:1142	BINDING SITE FOR RESIDUE SO4 A 902
4	AC4	SOFTWARE	HIS A:24 , ALA A:27 , PRO A:243 , HOH A:987 , HOH A:1070 , HOH A:1151 , HOH A:1176	BINDING SITE FOR RESIDUE SO4 A 903

(no "SS Bond" information available for 2DP3)

(no "Cis Peptide Bond" information available for 2DP3)

(no "SAP(SNP)/Variant" information available for 2DP3)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPI1_GIAIN	5-251	1	A:5-251
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPI1_GIAIN	168-178	1	A:168-178

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.	TPI1_GIAIN	5-251	2	A:5-251
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPI1_GIAIN	168-178	2	A:168-178

(no "Exon" information available for 2DP3)

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
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Chain A from PDB  Type:PROTEIN  Length:255
 aligned with TPI1_GIAIN | P36186 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
           TPI1_GIAIN     2 PARRPFIGGNFKCNGSLDFIKSHVAAIAAHKIPDSVDVVIAPSAVHLSTAIAANTSKQLRIAAQNVYLEGNGAWTGETSVEMLQDMGLKHVIVGHSERRRIMGETDEQSAKKAKRALEKGMTVIFCVGETLDERKANRTMEVNIAQLEALGKELGESKMLWKEVVIAYEPVWSIGTGVVATPEQAEEVHVGLRKWFAEKVCAEGAQHIRIIYGGSANGSNCEKLGQCPNIDGFLVGGASLKPEFMTMIDILTKTR 256
               SCOP domains d2dp3a_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2dp3A00 A:2-256 Aldolase class I                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhh.....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee......hhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TIM_2  PDB: A:5-251 UniProt: 5-251                                                                                                                                                                                                                     ----- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      ------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dp3 A   2 PARRPFIGGNFKCNGSLDFIKSHVAAIAAHKIPDSVDVVIAPSAVHLSTAIAANTSKQLRIAAQNVYLEGNGAWTGETSVEMLQDMGLKHVIVGHSERRRIMGETDEQSAKKAKRALEKGMTVIFCVGETLDERKANRTMEVNIAQLEALGKELGESKMLWKEVVIAYEPVWSIGTGVVATPEQAEEVHVGLRKWFVEKVAAEGAQHIRIIYGGSANGSNCEKLGQCPNIDGFLVGGASLKPEFMTMIDILTKTR 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

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: automated matches (20)

Protein domain: automated matches (20)

Giardia intestinalis [TaxId: 5741] (5)

d2dp3a_

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)

Giardia intestinalis. Organism_taxid: 5741. Strain: wb strain. (1)

2dp3A00

A:2-256

(no "Pfam Domain" information available for 2DP3)

Asymmetric Unit(hide GO term definitions)

Chain A (TPI1_GIAIN | P36186)

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: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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