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(-) Description

Title :  CRYSTALLOGRAPHIC BINDING STUDIES WITH AN ENGINEERED MONOMERIC VARIANT OF TRIOSEPHOSPHATE ISOMERASE
 
Authors :  M. Salin, E. G. Kapetaniou, M. Vaismaa, M. Lajunen, M. G. Casteleijn, P. L. Salmon, R. Wierenga
Date :  13 Jan 10  (Deposition) - 26 Jan 10  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Fatty Acid Biosynthesis, Gluconeogenesis, Glycolysis, Glycosome, Isomerase, Lipid Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Salin, E. G. Kapetaniou, M. Vaismaa, M. Lajunen, M. G. Casteleijn, P. Neubauer, L. Salmon, R. Wierenga
Crystallographic Binding Studies With An Engineered Monomeric Variant Of Triosephosphate Isomerase
Acta Crystallogr. , Sect. D V. 66 934 2010
PubMed-ID: 20693693  |  Reference-DOI: 10.1107/S0907444910025710

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
    ChainsA, B
    EC Number5.3.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainBL21 PLYSS
    Expression System Taxid511693
    FragmentRESIDUES 2-13,15-72,80-234,238-250
    MutationYES
    Organism ScientificTRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid5702
    Other DetailsA MONOMERIC MUTANT OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, WHICH HAS A BOUND 3PGA MOLECULE IN AN ACTIVE SITE
    SynonymTRIOSEPHOSPHATE ISOMERASE, TIM

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
13PG-1Ligand/Ion3-PHOSPHOGLYCERIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:11 , HIS B:95 , GLU B:167 , ALA B:171 , GLY B:173 , GLY B:212 , SER B:213 , LEU B:232 , ALA B:233 , GLY B:234 , HOH B:2260 , HOH B:2287BINDING SITE FOR RESIDUE 3PG B 1251

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X2G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X2G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X2G)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_TRYBB5-248
 
  2A:5-248
B:5-248
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_TRYBB165-175
 
  2A:165-175
B:165-175
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_TRYBB5-248
 
  1A:5-248
-
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_TRYBB165-175
 
  1A:165-175
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_TRYBB5-248
 
  1-
B:5-248
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_TRYBB165-175
 
  1-
B:165-175

(-) Exons   (0, 0)

(no "Exon" information available for 2X2G)

(-) Sequences/Alignments

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:233
 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 d2x2ga_ A:       Triosephosphate isomerase                                                                                                                                                                                                                SCOP domains
               CATH domains 2x2gA00 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.hhhhhhhhhhhhhhhh.hhhhhh.eeeee.hhhhh......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
                 2x2g A   2 SKPQPIAAANW------DSLSELIDLFNSTSINHDVQCVVASTFVHLAMTKERLSHPKFVIAAQNAGNADA-------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         
                                     12     19                                                   72      80                                                                                                                                                       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 d2x2gb_ B: T riosephosphate isomerase                                                                                                                                                                                                                     SCOP domains
               CATH domains 2x2gB00 B:2- 250 Aldolase class I                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) ----TIM-2x2g B01 B:6-246                                                                                                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) ----TIM-2x2g B02 B:6-246                                                                                                                                                                                                                             ---- Pfam domains (2)
         Sec.struct. author .....eeeee..-.....hhhhhhhhhhhh......eeeee.hhhhhhhhhhhh....eeeeee...hhhh-------hhhhhhhh..eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhh.hhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhh.....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
                 2x2g 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (9, 9)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TPIS_TRYBB | P047891ag1 1dkw 1iig 1iih 1kv5 1ml1 1mss 1mtm 1tpd 1tpe 1tpf 1trd 1tri 1tsi 1tti 1ttj 2j24 2j27 2v0t 2v2c 2v2d 2v2h 2v5l 2vei 2vek 2vel 2vem 2ven 2wsq 2wsr 2x16 2x1r 2x1s 2x1t 2x1u 2y6z 2y70 3q37 3tim 4jeq 4pc8 4pcf 4tim 5i3f 5i3g 5i3h 5i3i 5i3j 5i3k 5tim 6tim

(-) Related Entries Specified in the PDB File

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
1ttj
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
2ven 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
2wsq MONOTIM MUTANT RMM0-1, DIMERIC FORM.
2wsr MONOTIM MUTANT RMM0-1, MONOMERIC FORM.
2x16 CRYSTALLOGRAPHIC BINDING STUDIES WITH AN ENGINEERED MONOMERIC VARIANT OF TRIOSEPHOSPHATE ISOMERASE
2x1r CRYSTALLOGRAPHIC BINDING STUDIES WITH AN ENGINEERED MONOMERIC VARIANT OF TRIOSEPHOSPHATE ISOMERASE
2x1s CRYSTALLOGRAPHIC BINDING STUDIES WITH AN ENGINEERED MONOMERIC VARIANT OF TRIOSEPHOSPHATE ISOMERASE
2x1t CRYSTALLOGRAPHIC BINDING STUDIES WITH AN ENGINEERED MONOMERIC VARIANT OF TRIOSEPHOSPHATE ISOMERASE
2x1u CRYSTALLOGRAPHIC BINDING STUDIES WITH AN ENGINEERED MONOMERIC VARIANT OF TRIOSEPHOSPHATE ISOMERASE
3tim TRIOSEPHOSPHATE ISOMERASE
4tim TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH 2- PHOSPHOGLYCERATE
5tim TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH SULFATE
6tim TRIOSEPHOSPHATE ISOMERASE COMPLEX WITH GLYCEROL -3-PHOSPHATE