2VEN - JenaLib

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Title :   STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES

Authors :   M. Alahuhta, M. Salin, M. G. Casteleijn, C. Kemmer, I. El-Sayed, K. Augu P. Neubauer, R. K. Wierenga

Date :   25 Oct 07 (Deposition) - 19 Feb 08 (Release) - 28 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Isomerase, Tim Barrel, Glycolysis, Pentose Shunt, Gluconeogenesis, Lipid Synthesis, Fatty Acid Biosynthesis, Glycosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Alahuhta, M. Salin, M. G. Casteleijn, C. Kemmer, I. El-Sayed, K. Augustyns, P. Neubauer, R. K. Wierenga
Structure-Based Protein Engineering Efforts With A Monomeric Tim Variant: The Importance Of A Single Point Mutation For Generating An Active Site With Suitable Binding Properties.
Protein Eng. Des. Sel. V. 21 257 2008
PubMed-ID: 18239072 | Reference-DOI: 10.1093/PROTEIN/GZN002

Molecule 1 - GLYCOSOMAL TRIOSEPHOSPHATE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-13,15-72,80-234,238-250
	Mutation	:	YES
	Organism Scientific	:	TRYPANOSOMA BRUCEI BRUCEI
	Organism Taxid	:	5702
	Synonym	:	TRIOSEPHOSPHATE ISOMERASE, TIM, TRIOSE-PHOSPHATE ISOMERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CIT	-1	Ligand/Ion	CITRIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN B:11 , LYS B:13 , HIS B:95 , GLU B:167 , ALA B:171 , GLY B:173 , SER B:213 , ALA B:233 , GLY B:234 , LYS B:239 , HOH B:2012 , HOH B:2195 , HOH B:2203	BINDING SITE FOR RESIDUE CIT B1251

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_TRYBB	5-248	2	A:5-248 B:5-248
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_TRYBB	165-175	2	A:165-170 B:165-175

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_TRYBB	5-248	1	A:5-248 -
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_TRYBB	165-175	1	A:165-170 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_TRYBB	5-248	1	- B:5-248
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_TRYBB	165-175	1	- B:165-175

(no "Exon" information available for 2VEN)

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:228
 aligned with TPIS_TRYBB | P04789 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
           TPIS_TRYBB     2 SKPQPIAAANWKCNGSQQSLSELIDLFNSTSINHDVQCVVASTFVHLAMTKERLSHPKFVIAAQNAIAKSGAFTGEVSLPILKDFGVNWIVLGHSERRAYYGETNEIVADKVAAAVASGFMVIACIGETLQERESGRTAVVVLTQIAAIAKKLKKADWAKVVIAYEPVWAIGTGKVATPQQAQEAHALIRSWVSSKIGADVAGELRILYGGSVNGKNARTLYQQRDVNGFLVGGASLKPEFVDIIKATQ 250
               SCOP domains d2vena_ A: T      riosephosphate isomerase                                                                                                                                                                                                                SCOP domains
               CATH domains 2venA00 A:2-      250 Aldolase class I                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..------hhhhhhhhhhh.......eeeee.hhhhhhhhhhhh....eeeeee...hhhh-------hhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh..hhhhhh.eeeee....-----...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....hhhhhhhhhh.....eeeee---...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TIM_2  PDB: A:5-248 UniProt: 5-248                                                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ven A   2 SKPQPIAAANWK------SLSELIDLFNSTSINHDVQCVVASTFVHLAMTKERLSHPKFVIAAQNAGNADA-------LASLKDFGVNWIVLGHSERRWYYGETNEIVADKVAAAVASGFMVIACIGETLQERESGRTAVVVLTQIAAIAKKLKKADWAKVVIAYEPVW-----KVATPQQAQEAHALIRSWVSSKIGADVAGELRILYGGSVNGKNARTLYQQRDVNGFLAG---LKPEFVDIIKATQ 250
                                    11 |      21        31        41        51        61        71|       81        91       101       111       121       131       141       151       161        |-    |  181       191       201       211       221       231  |   |241         
                                      13     20                                                  72      80                                                                                       170   176                                                       234 238

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with TPIS_TRYBB | P04789 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
           TPIS_TRYBB     2 SKPQPIAAANWKCNGSQQSLSELIDLFNSTSINHDVQCVVASTFVHLAMTKERLSHPKFVIAAQNAIAKSGAFTGEVSLPILKDFGVNWIVLGHSERRAYYGETNEIVADKVAAAVASGFMVIACIGETLQERESGRTAVVVLTQIAAIAKKLKKADWAKVVIAYEPVWAIGTGKVATPQQAQEAHALIRSWVSSKIGADVAGELRILYGGSVNGKNARTLYQQRDVNGFLVGGASLKPEFVDIIKATQ 250
               SCOP domains d2venb_ B: T riosephosphate isomerase                                                                                                                                                                                                                     SCOP domains
               CATH domains 2venB00 B:2- 250 Aldolase class I                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) ----TIM-2ven B01 B:6-246                                                                                                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) ----TIM-2ven B02 B:6-246                                                                                                                                                                                                                             ---- Pfam domains (2)
         Sec.struct. author .....eeeee..-.....hhhhhhhhhhh.......eeeee.hhhhhhhhhhhh....eeeeee...hhhh-------hhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhh.hhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhh.....eeeee---...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TIM_2  PDB: B:5-248 UniProt: 5-248                                                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ven B   2 SKPQPIAAANWK-SGSPDSLSELIDLFNSTSINHDVQCVVASTFVHLAMTKERLSHPKFVIAAQNAGNADA-------LASLKDFGVNWIVLGHSERRWYYGETNEIVADKVAAAVASGFMVIACIGETLQERESGRTAVVVLTQIAAIAKKLKKADWAKVVIAYEPVWAIGTGKVATPQQAQEAHALIRSWVSSKIGADVAGELRILYGGSVNGKNARTLYQQRDVNGFLAG---LKPEFVDIIKATQ 250
                                    11 | |    21        31        41        51        61        71|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  |   |241         
                                      13 |                                                       72      80                                                                                                                                                       234 238            
                                        15

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)

Trypanosome (Trypanosoma brucei) [TaxId: 5691] (41)

1a	d2vena_	A:
1b	d2venb_	B:

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)

Trypanosoma brucei brucei. Organism_taxid: 5702. (20)

1a	2venB00	B:2-250
1b	2venA00	A:2-250

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: TIM (80)

Trypanosoma brucei brucei (28)

1a	TIM-2venB01	B:6-246
1b	TIM-2venB02	B:6-246

Asymmetric Unit(hide GO term definitions)

Chain A,B (TPIS_TRYBB | P04789)

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.
cellular component
	GO:0020015	glycosome	A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Asymmetric Unit
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	2ven
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	5.3.1.1
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1ag1	MONOHYDROGEN PHOSPHATE BINDING TO TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE
1dkw	CRYSTAL STRUCTURE OF TRIOSE-PHOSPHATE ISOMERASE WITH MODIFIED SUBSTRATE BINDING SITE
1iig	STRUCTURE OF TRYPANOSOMA BRUCEI BRUCEI TRIOSEPHOSPHATEISOMERASE COMPLEXED WITH 3- PHOSPHONOPROPIONATE
1iih	STRUCTURE OF TRYPANOSOMA BRUCEI BRUCEI TRIOSEPHOSPHATEISOMERASE COMPLEXED WITH 3- PHOSPHOGLYCERATE
1kv5	STRUCTURE OF TRYPANOSOMA BRUCEI BRUCEI TIM WITH THE SALT-BRIDGE-FORMING RESIDUE ARG191 MUTATED TO SER
1ml1	PROTEIN ENGINEERING WITH MONOMERIC TRIOSEPHOSPHATEISOMERASE: THE MODELLING AND STRUCTURE VERIFICATION OFA SEVEN RESIDUE LOOP
1mss	TRIOSEPHOSPHATE ISOMERASE MUTANT WITH PHE 45 REPLACED BY SER, VAL 46 REPLACED BY SER, AND RESIDUES 68 - 82 REPLACED BY THE RESIDUES GNADALAS (F45S,V46S,68-82:GNADALAS)
1mtm	LOOP-1 MODELING OF MONOTIM-A100W MUTANT
1tpd	TRIOSEPHOSPHATE ISOMERASE
1tpe	TRIOSEPHOSPHATE ISOMERASE
1tpf	TRIOSEPHOSPHATE ISOMERASE
1trd	TRIOSEPHOSPHATE ISOMERASE 1
1tri	TRIOSEPHOSPHATE ISOMERASE MUTANT WITH 15 RESIDUES (68 - 82) REPLACED BY 8 RESIDUES
1tsi	TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH N- HYDROXY-4-PHOSPHONO-BUTANAMIDE
1tti	MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE ; CHAIN: NULL; EC: 5.3.1.1; ENGINEERED: YES; MUTATION: I68G, A69N, K70A, S71D, DEL( 73-79), P81A, A100W; OTHER_DETAILS: MONOTIM WITH A110W MUTATION
1ttj	MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE ; CHAIN: NULL; EC: 5.3.1.1; MUTATION: VARIANT OF MONOTIM WITH PHE 45 REPLACED BY SER AND VAL 46 REPLACED BY SER (F45S, V46S) AND 73 - 79 DELETED
2j24	THE FUNCTIONAL ROLE OF THE CONSERVED ACTIVE SITE PROLINE OF TRIOSEPHOSPHATE ISOMERASE
2j27	THE FUNCTIONAL ROLE OF THE CONSERVED ACTIVE SITE PROLINE OF TRIOSEPHOSPHATE ISOMERASE
2v0t	THE A178L MUTATION IN THE C-TERMINAL HINGE OF THE FLEXIBLE LOOP-6 OF TRIOSEPHOSPHATE ISOMERASE (TIM) INDUCES A MORE CLOSED CONFORMATION OF THIS HINGE REGION IN DIMERIC AND MONOMERIC TIM
2v2c	THE A178L MUTATION IN THE C-TERMINAL HINGE OF THE FLEXIBLE LOOP-6 OF TRIOSEPHOSPHATE ISOMERASE (TIM) INDUCES A MORE CLOSED CONFORMATION OF THIS HINGE REGION IN DIMERIC AND MONOMERIC TIM
2v2d	THE A178L MUTATION IN THE C-TERMINAL HINGE OF THE FLEXIBLE LOOP-6 OF TRIOSEPHOSPHATE ISOMERASE (TIM) INDUCES A MORE CLOSED CONFORMATION OF THIS HINGE REGION IN DIMERIC AND MONOMERIC TIM
2v2h	THE A178L MUTATION IN THE C-TERMINAL HINGE OF THE FLEXIBLE LOOP-6 OF TRIOSEPHOSPHATE ISOMERASE (TIM) INDUCES A MORE CLOSED CONFORMATION OF THIS HINGE REGION IN DIMERIC AND MONOMERIC TIM
2v5l	STRUCTURES OF THE OPEN AND CLOSED STATE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE: AS OBSERVED IN A NEW CRYSTAL FORM: IMPLICATIONS FOR THE REACTION MECHANISM
2vei	STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES
2vek	STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES
2vel	STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES
2vem	STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES
3tim	TRIOSEPHOSPHATE ISOMERASE
4tim	TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH 2- PHOSPHOGLYCERATE
5tim	TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH SULFATE
6tim	TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH GLYCEROL -3-PHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

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 (1, 2)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

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Related Entries Specified in the PDB File