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(-) Description

Title :  0.83A RESOLUTION STRUCTURE OF THE E65Q MUTANT OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE COMPLEXED WITH 2-PHOSPHOGLYCOLATE
 
Authors :  I. Kursula, R. K. Wierenga
Date :  04 Nov 02  (Deposition) - 21 Jan 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.83
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tim, Atomic Resolution, Enzyme-Ligand Complex, Transition-State Analogue, Low-Barrier Hydrogen Bond, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Kursula, R. K. Wierenga
Crystal Structure Of Triosephosphate Isomerase Complexed With 2-Phosphoglycolate At 0. 83-A Resolution
J. Biol. Chem. V. 278 9544 2003
PubMed-ID: 12522213  |  Reference-DOI: 10.1074/JBC.M211389200

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    Chains: A
    EC Number: 5.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: LEISHMANIA MEXICANA
    Organism Taxid: 5665
    Synonym: TIM

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2GOL3Ligand/IonGLYCEROL
3PGA1Ligand/Ion2-PHOSPHOGLYCOLIC ACID
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2GOL6Ligand/IonGLYCEROL
3PGA2Ligand/Ion2-PHOSPHOGLYCOLIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:11 , LYS A:13 , HIS A:95 , GLU A:167 , ALA A:171 , ILE A:172 , GLY A:173 , GLY A:212 , SER A:213 , LEU A:232 , GLY A:234 , GLY A:235 , HOH A:803 , HOH A:810 , HOH A:846 , HOH A:988BINDING SITE FOR RESIDUE PGA A 650
2AC2SOFTWARELYS A:84 , GLN A:119 , GLY A:120 , TRP A:193 , GOL A:800 , HOH A:854 , HOH A:1137 , HOH A:1262BINDING SITE FOR RESIDUE ACY A 700
3AC3SOFTWAREARG A:134 , ASN A:137 , GLN A:138 , THR A:139 , HOH A:963 , HOH A:1256BINDING SITE FOR RESIDUE ACY A 701
4AC4SOFTWARELEU A:144 , SER A:145 , SER A:148 , GLN A:161 , TRP A:193 , ACY A:700 , HOH A:834 , HOH A:1106 , HOH A:1144 , HOH A:1252BINDING SITE FOR RESIDUE GOL A 800
5AC5SOFTWAREPHE A:45 , ASN A:66 , GLY A:76 , GLU A:77 , ARG A:98 , HOH A:809 , HOH A:860 , HOH A:1332 , HOH A:1360BINDING SITE FOR RESIDUE GOL A 801
6AC6SOFTWARETRP A:170 , LYS A:176 , ASP A:244 , HOH A:896 , HOH A:1092 , HOH A:1173 , HOH A:1227 , HOH A:1264BINDING SITE FOR RESIDUE GOL A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N55)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N55)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N55)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_LEIME6-249  1A:5-248
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_LEIME166-176  1A:165-175
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_LEIME6-249  2A:5-248
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_LEIME166-176  2A:165-175

(-) Exons   (0, 0)

(no "Exon" information available for 1N55)

(-) 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_LEIME | P48499 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:249
                                    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_LEIME     3 AKPQPIAAANWKCNGTTASIEKLVQVFNEHTISHDVQCVVAPTFVHIPLVQAKLRNPKYVISAENAIAKSGAFTGEVSMPILKDIGVHWVILGHSERRTYYGETDEIVAQKVSEACKQGFMVIACIGETLQQREANQTAKVVLSQTSAIAAKLTKDAWNQVVLAYEPVWAIGTGKVATPEQAQEVHLLLRKWVSENIGTDVAAKLRILYGGSVNAANAATLYAKPDINGFLVGGASLKPEFRDIIDATR 251
               SCOP domains d1n55a_ A: Triosephosphate isomerase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1n55A00 A:2-250 Aldolase class I                                                                                                                                                                                                                          CATH domains
               Pfam domains ----TIM-1n55A01 A:6-246                                                                                                                                                                                                                              ---- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhh....eeeee..............hhhhhhhhh..eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee......hhhhhhh.....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TIM_2  PDB: A:5-248 UniProt: 6-249                                                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n55 A   2 AKPQPIAAANWKCNGTTASIEKLVQVFNEHTISHDVQCVVAPTFVHIPLVQAKLRNPKYVISAQNAIAKSGAFTGEVSMPILKDIGVHWVILGHSERRTYYGETDEIVAQKVSEACKQGFMVIACIGETLQQREANQTAKVVLSQTSAIAAKLTKDAWNQVVLAYEPVWAIGTGKVATPEQAQEVHLLLRKWVSENIGTDVAAKLRILYGGSVNAANAATLYAKPDINGFLVGGASLKPEFRDIIDATR 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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (TPIS_LEIME | P48499)
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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_LEIME | P48499: 1amk 1if2 1qds 2vxn 2y61 2y62 2y63

(-) Related Entries Specified in the PDB File

1if2 L.MEXICANA TIM E65Q MUTANT COMPLEXED WITH IPP
1qds L.MEXICANA TIM E65Q MUTANT COMPLEXED WITH 2- PHOSPHOGLYCOLATE AT 2A RESOLUTION