Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  LARGE SCALE STRUCTURAL REARRANGEMENTS OF THE FRONT LOOPS IN MONOMERISED TRIOSEPHOSPHATE ISOMERASE, AS DEDUCED FROM THE COMPARISON OF THE STRUCTURAL PROPERTIES OF MONOTIM AND ITS POINT MUTATION VARIANT MONOSS
 
Authors :  K. V. Radha Kishan, R. K. Wierenga
Date :  27 Jul 94  (Deposition) - 30 Sep 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase(Intramolecular Oxidoreductase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. V. Borchert, K. V. Kishan, J. P. Zeelen, W. Schliebs, N. Thanki, R. Abagyan, R. Jaenicke, R. K. Wierenga
Three New Crystal Structures Of Point Mutation Variants Of Monotim: Conformational Flexibility Of Loop-1, Loop-4 And Loop-8.
Structure V. 3 669 1995
PubMed-ID: 8591044  |  Reference-DOI: 10.1016/S0969-2126(01)00202-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.1
    Engineered: YES
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 5702
    Strain: BRUCEI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1MSS)

(-) Sites  (0, 0)

(no "Site" information available for 1MSS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological 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

(-) Exons   (0, 0)

(no "Exon" information available for 1MSS)

(-) 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:242
 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 d1mssa_ A: Triosephosphate isomerase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1mssA00 A:2-250 Aldolase class I                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhh....eeeeee...hhhh-------hhhhhhhh..eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh....hhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhh.....eeeee.hhhhhhhhhhhhhh. 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
                 1mss A   2 SKPQPIAAANWKCNGSQQSLSELIDLFNSTSINHDVQCVVASTSSHLAMTKERLSHPKFVIAAQNAGNADA-------LASLKDFGVNWIVLGHSERRAYYGETNEIVADKVAAAVASGFMVIACIGETLQERESGRTAVVVLTQIAAIAKKLKKADWAKVVIAYEPVWAIGTGKVATPQQAQEAHALIRSWVSSKIGADVAGELRILYGGSVNGKNARTLYQQRDVNGFLVGGASLKPEFVDIIKATQ 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         
                                                                                                 72      80                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:242
 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 d1mssb_ B: Triosephosphate isomerase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1mssB00 B:2-250 Aldolase class I                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) ----TIM-1mssB01 B:6-246                                                                                                                                                                                                                              ---- Pfam domains (1)
           Pfam domains (2) ----TIM-1mssB02 B:6-246                                                                                                                                                                                                                              ---- Pfam domains (2)
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhh......eeeee....hhhhhhhhh......eee....hhhh-------hhhhhhhh..eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhh...hhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......hhhhhhhh....eeeee.hhhhhhhhhhhhh.. 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
                 1mss B   2 SKPQPIAAANWKCNGSQQSLSELIDLFNSTSINHDVQCVVASTSSHLAMTKERLSHPKFVIAAQNAGNADA-------LASLKDFGVNWIVLGHSERRAYYGETNEIVADKVAAAVASGFMVIACIGETLQERESGRTAVVVLTQIAAIAKKLKKADWAKVVIAYEPVWAIGTGKVATPQQAQEAHALIRSWVSSKIGADVAGELRILYGGSVNGKNARTLYQQRDVNGFLVGGASLKPEFVDIIKATQ 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         
                                                                                                 72      80
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1mss)
 
  Sites
(no "Sites" information available for 1mss)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1mss)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1mss
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TPIS_TRYBB | P04789
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.3.1.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TPIS_TRYBB | P04789
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TPIS_TRYBB | P04789: 1ag1 1dkw 1iig 1iih 1kv5 1ml1 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 2x2g 2y6z 2y70 3q37 3tim 4jeq 4pc8 4pcf 4tim 5i3f 5i3g 5i3h 5i3i 5i3j 5i3k 5tim 6tim

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1MSS)