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(-) Description

Title :  THE INFLUENCE OF CRYSTAL PACKING ON CRYSTALLOGRAPHIC BINDING STUDIES: A NEW CRYSTAL FORM OF TRYPANOSOMAL TIM
 
Authors :  M. E. M. Noble, R. K. Wierenga
Date :  06 Oct 92  (Deposition) - 31 Oct 93  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  B  (2x)
Keywords :  Intramolecular Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. E. Noble, J. P. Zeelen, R. K. Wierenga
Structures Of The "Open" And "Closed" State Of Trypanosomal Triosephosphate Isomerase, As Observed In A New Crystal Form: Implications For The Reaction Mechanism.
Proteins V. 16 311 1993
PubMed-ID: 8356028  |  Reference-DOI: 10.1002/PROT.340160402

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    ChainsA, B
    EC Number5.3.1.1
    EngineeredYES
    Organism ScientificTRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid5702
    StrainBRUCEI

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (2x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PGH1Ligand/IonPHOSPHOGLYCOLOHYDROXAMIC ACID
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1PGH-1Ligand/IonPHOSPHOGLYCOLOHYDROXAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PGH1Ligand/IonPHOSPHOGLYCOLOHYDROXAMIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1PGH2Ligand/IonPHOSPHOGLYCOLOHYDROXAMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:11 , LYS B:13 , HIS B:95 , GLU B:167 , GLY B:173 , SER B:213 , LEU B:232 , GLY B:234 , GLY B:235 , HOH B:306 , HOH B:359BINDING SITE FOR RESIDUE PGH B 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_TRYBB5-248
 
  2A:5-248
-
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_TRYBB165-175
 
  2A: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
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_TRYBB5-248
 
  2-
B:5-248
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_TRYBB165-175
 
  2-
B:165-175

(-) Exons   (0, 0)

(no "Exon" information available for 1TRD)

(-) 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:249
 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 d1trda_ A: Triosephosphate isomerase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1trdA00 A:2-250 Aldolase class I                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhh.......eeeeee...hhhhhhhhh....eeeee..............hhhhhhhhh..eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhh..hhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhh.....eeeehhhhhhhhhhhhhhh.. 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
                 1trd A   2 SKPQPIAAANWKCNGSQQSLSELIDLFNSTSINHDVQCVVASTFVHLAMTKERLSHPKFVIAAQNAIAKSGAFTGEVSLPILKDFGVNWIVLGHSERRAYYGETNEIVADKVAAAVASGFMVIACIGETLQERESGRTAVVVLTQIAAIAKKLKKADWAKVVIAYEPVWAIGTGKVATPQQAQEAHALIRSWVSSKIGADVAGELRILYGGSVNGKNARTLYQQRDVNGFLVGGASLKPEFVDIIKATQ 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         

Chain B from PDB  Type:PROTEIN  Length:249
 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 d1trdb_ B: Triosephosphate isomerase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1trdB00 B:2-250 Aldolase class I                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) ----TIM-1trdB01 B:6-246                                                                                                                                                                                                                              ---- Pfam domains (1)
           Pfam domains (2) ----TIM-1trdB02 B:6-246                                                                                                                                                                                                                              ---- Pfam domains (2)
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhh.......eeeeee...hhhhhhhhh....eeeee..............hhhhhhhhh..eeee.hhhhhhh...hhhhhhhhhhhhhh...eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhh.....eeeehhhhhhhhhhhhhh... 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
                 1trd B   2 SKPQPIAAANWKCNGSQQSLSELIDLFNSTSINHDVQCVVASTFVHLAMTKERLSHPKFVIAAQNAIAKSGAFTGEVSLPILKDFGVNWIVLGHSERRAYYGETNEIVADKVAAAVASGFMVIACIGETLQERESGRTAVVVLTQIAAIAKKLKKADWAKVVIAYEPVWAIGTGKVATPQQAQEAHALIRSWVSSKIGADVAGELRILYGGSVNGKNARTLYQQRDVNGFLVGGASLKPEFVDIIKATQ 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         

   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 1tri 1tsi 1tti 1ttj 2j24 2j27 2v0t 2v2c 2v2d 2v2h 2v5l 2vei 2vek 2vel 2vem 2ven 2wsq 2wsr 2x16 2x1r 2x1s 2x1t 2x1u 2x2g 2y6z 2y70 3q37 3tim 4jeq 4pc8 4pcf 4tim 5i3f 5i3g 5i3h 5i3i 5i3j 5i3k 5tim 6tim

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