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(-) Description

Title :  DHAP BOUND LEPTOSPIRA INTERROGANS TRIOSEPHOSPHATE ISOMERASE (LITIM)
 
Authors :  V. Pareek, P. Balaram, M. R. N. Murthy
Date :  08 Mar 15  (Deposition) - 09 Mar 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrels, Beta-Alpha Barrels, Isomerase, Dihydroxyacetone Phosphate, Glycolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Pareek, M. Samanta, N. V. Joshi, H. Balaram, M. R. N. Murthy, P. Balaram
Connecting Active-Site Loop Conformations And Catalysis In Triosephosphate Isomerase: Insights From A Rare Variation A Residue 96 In The Plasmodial Enzyme
Chembiochem V. 17 620 2016
PubMed-ID: 26762569  |  Reference-DOI: 10.1002/CBIC.201500532

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: AA200
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LEP2GSC113_RS0110880
    Organism Scientific: LEPTOSPIRA INTERROGANS SEROVAR ICTEROHAEMORRHAGIAE STR. RGA
    Organism Taxid: 1291351
    Strain: RGA
    Synonym: TIM,TRIOSE-PHOSPHATE ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
113P2Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2EDO15Ligand/Ion1,2-ETHANEDIOL
3SO42Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:10 , LYS A:12 , HIS A:97 , GLU A:169 , ALA A:173 , ILE A:174 , GLY A:175 , SER A:217 , LEU A:236 , GLY A:238 , GLY A:239 , SO4 A:302 , HOH A:451 , HOH A:456 , HOH A:537 , HOH A:548 , HOH A:551 , HOH A:552binding site for residue 13P A 301
02AC2SOFTWARELYS A:12 , ALA A:173 , ILE A:174 , GLY A:175 , GLY A:216 , SER A:217 , GLY A:238 , GLY A:239 , 13P A:301 , HOH A:451 , HOH A:456 , HOH A:537 , HOH A:548binding site for residue SO4 A 302
03AC3SOFTWAREGLU A:50 , ASN A:51 , GLU B:50 , ASN B:51binding site for residue EDO A 303
04AC4SOFTWAREARG A:116 , ILE A:156 , PHE A:160binding site for residue EDO A 304
05AC5SOFTWARESER A:204 , GLU A:208 , HOH A:401 , ARG B:136 , GLN B:184binding site for residue EDO A 305
06AC6SOFTWARESER A:146 , SER A:147 , ARG A:150 , GLU A:151 , HOH A:463binding site for residue EDO A 306
07AC7SOFTWARELYS A:4 , SER A:162 , LEU A:164 , ILE A:210 , SER A:211binding site for residue EDO A 307
08AC8SOFTWAREPRO A:220 , ASP A:221 , ASN A:222 , ILE A:223 , GLN A:224 , ASP A:225binding site for residue EDO A 308
09AC9SOFTWARELEU A:104 , HOH A:553 , GLY B:105binding site for residue EDO A 309
10AD1SOFTWAREGLU A:143 , PHE A:191 , HOH A:419binding site for residue EDO A 310
11AD2SOFTWARELEU B:133 , TRP B:172 , GLN B:184binding site for residue EDO A 311
12AD3SOFTWAREASN B:10 , LYS B:12 , HIS B:97 , GLU B:169 , ALA B:173 , ILE B:174 , GLY B:175 , SER B:217 , LEU B:236 , GLY B:238 , GLY B:239 , SO4 B:302 , HOH B:444 , HOH B:501 , HOH B:532 , HOH B:533 , HOH B:534binding site for residue 13P B 301
13AD4SOFTWAREALA B:173 , ILE B:174 , GLY B:175 , SER B:217 , GLY B:238 , GLY B:239 , 13P B:301 , HOH B:444 , HOH B:501 , HOH B:532 , HOH B:533 , HOH B:534binding site for residue SO4 B 302
14AD5SOFTWAREARG B:116 , LYS B:120 , PHE B:160 , HOH B:450 , HOH B:524binding site for residue EDO B 303
15AD6SOFTWAREARG A:136 , GLN A:184 , GLY B:202 , EDO B:305 , HOH B:405binding site for residue EDO B 304
16AD7SOFTWARETRP A:172 , LYS A:178 , GLN A:184 , EDO B:304 , HOH B:404binding site for residue EDO B 305
17AD8SOFTWAREVAL B:159binding site for residue EDO B 306
18AD9SOFTWAREHIS B:70 , PHE B:117 , HOH B:539binding site for residue EDO B 307
19AE1SOFTWAREHOH A:431 , HOH A:553 , PHE B:103binding site for residue EDO B 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YMZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YMZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YMZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YMZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4YMZ)

(-) Sequences/Alignments

Asymmetric/Biological 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh...eeeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhh...hhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhh....hhhhhh...eeee...hhhhhhhhhh.....eeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ymz A   2 ARKTIIAGNWKMNLSLKEAVFLAHSIREKIPSISKDKVSMVFPSTLHLENVSKILEGSSVIVGAQNCYHSGLAAFTGETSPDQLKEIGVKVVMVGHSERRQFLGESNFFCNDKIRFLLKNEFTVLYCVGETLSERESGKTLEVLSSQIREGLKGIDSVFFSNLILAYEPVWAIGTGKVATPSQAQEVHSFIRKEISGLFVGASSISESISILYGGSVKPDNIQDLLKEKDIDGGLVGGASQKISSFAGLF 251
                                    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


Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhh...hhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhh.eeee......hhhhhhh.....eeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ymz B   2 ARKTIIAGNWKMNLSLKEAVFLAHSIREKIPSISKDKVSMVFPSTLHLENVSKILEGSSVIVGAQNCYHSGLAAFTGETSPDQLKEIGVKVVMVGHSERRQFLGESNFFCNDKIRFLLKNEFTVLYCVGETLSERESGKTLEVLSSQIREGLKGIDSVFFSNLILAYEPVWAIGTGKVATPSQAQEVHSFIRKEISGLFVGASSISESISILYGGSVKPDNIQDLLKEKDIDGGLVGGASQKISSFAGLF 251
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4YMZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YMZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YMZ)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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4x22 APO FORM STRUCTURE OF THE SAME ENZYME