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Title :   STRUCTURAL GENOMICS OF CAENORHABDITIS ELEGANS: TRIOSE PHOSPHATE ISOMERASE

Authors :   J. Symersky, S. Li, J. Finley, Z. -J. Liu, H. Qui, C. H. Luan, M. Carson, J. Tsao, D. Johnson, G. Lin, J. Zhao, W. Thomas, L. A. Nagy, B. Sha, L. J. Delucas, B. -C. Wang, M. Luo, Southeast Collaboratory For Structural Genomics (Secsg)

Date :   06 Sep 02 (Deposition) - 13 Sep 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Triose Phosphate Isomerase, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Symersky, S. Li, M. Carson, M. Luo
Structural Genomics Of Caenorhabditis Elegans: Triosephosphate Isomerase
Proteins V. 51 484 2003
PubMed-ID: 12696058 | Reference-DOI: 10.1002/PROT.10364
(for further references see the PDB file header)

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST 17.1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239
	Synonym	:	TIM

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:10 , LYS A:12 , HIS A:94 , GLU A:164 , LEU A:229 , VAL A:230 , GLY A:231 , SO4 A:901	BINDING SITE FOR RESIDUE ACT A 906
2	AC2	SOFTWARE	ASN B:10 , LYS B:12 , HIS B:94 , GLU B:164 , LEU B:229 , VAL B:230 , GLY B:231 , SO4 B:902	BINDING SITE FOR RESIDUE ACT B 907
3	AC3	SOFTWARE	LYS A:12 , GLU A:164 , ALA A:168 , ILE A:169 , GLY A:170 , SER A:210 , GLY A:231 , GLY A:232 , ACT A:906 , HOH A:931 , HOH A:936 , HOH A:978 , HOH A:996	BINDING SITE FOR RESIDUE SO4 A 901
4	AC4	SOFTWARE	LYS B:12 , GLU B:164 , ALA B:168 , ILE B:169 , GLY B:170 , SER B:210 , GLY B:231 , GLY B:232 , ACT B:907 , HOH B:912 , HOH B:922 , HOH B:952 , HOH B:988	BINDING SITE FOR RESIDUE SO4 B 902
5	AC5	SOFTWARE	THR A:25 , ASN A:28 , HOH A:1018 , HOH A:1054 , HOH A:1055 , HOH A:1058	BINDING SITE FOR RESIDUE SO4 A 903
6	AC6	SOFTWARE	ARG A:133 , GLN A:179	BINDING SITE FOR RESIDUE SO4 A 904
7	AC7	SOFTWARE	ARG B:133 , GLN B:179 , HOH B:1094	BINDING SITE FOR RESIDUE SO4 B 905

(no "SS Bond" information available for 1MO0)

(no "Cis Peptide Bond" information available for 1MO0)

(no "SAP(SNP)/Variant" information available for 1MO0)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_CAEEL	4-245	2	A:4-245 B:4-245
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_CAEEL	162-172	2	A:162-172 B:162-172

(no "Exon" information available for 1MO0)

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
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Chain A from PDB  Type:PROTEIN  Length:257
 aligned with TPIS_CAEEL | Q10657 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:257
                                    1                                                                                                                                                                                                                                                   247  
                                    |2        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_CAEEL     - --------MTRKFFVGGNWKMNGDYASVDGIVTFLNASADNSSVDVVVAPPAPYLAYAKSKLKAGVLVAAQNCYKVPKGAFTGEISPAMIKDLGLEWVILGHSERRHVFGESDALIAEKTVHALEAGIKVVFCIGEKLEEREAGHTKDVNFRQLQAIVDKGVSWENIVIAYEPVWAIGTGKTASGEQAQEVHEWIRAFLKEKVSPAVADATRIIYGGSVTADNAAELGKKPDIDGFLVGGASLKPDFVKIINARS--   -
               SCOP domains d1mo0a_ A: Triosephosphate isomerase                                                                                                                                                                                                                              SCOP domains
               CATH domains 1mo0A00 A:-7-249 Aldolase class I                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh...eeeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh.......eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......hhhhhh......eeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------TIM_2  PDB: A:4-245 UniProt: 4-245                                                                                                                                                                                                                ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      ----------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mo0 A  -7 STSLYKAGLTRKFFVGGNWKMNGDYASVDGIVTFLNASADNSSVDVVVAPPAPYLAYAKSKLKAGVLVAAQNCYKVPKGAFTGEISPAMIKDLGLEWVILGHSERRHVFGESDALIAEKTVHALEAGIKVVFCIGEKLEEREAGHTKDVNFRQLQAIVDKGVSWENIVIAYEPVWAIGTGKTASGEQAQEVHEWIRAFLKEKVSPAVADATRIIYGGSVTADNAAELGKKPDIDGFLVGGASLKPDFVKIINARSTA 249
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with TPIS_CAEEL | Q10657 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:245
                                    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_CAEEL     3 RKFFVGGNWKMNGDYASVDGIVTFLNASADNSSVDVVVAPPAPYLAYAKSKLKAGVLVAAQNCYKVPKGAFTGEISPAMIKDLGLEWVILGHSERRHVFGESDALIAEKTVHALEAGIKVVFCIGEKLEEREAGHTKDVNFRQLQAIVDKGVSWENIVIAYEPVWAIGTGKTASGEQAQEVHEWIRAFLKEKVSPAVADATRIIYGGSVTADNAAELGKKPDIDGFLVGGASLKPDFVKIINARS 247
               SCOP domains d1mo0b_ B: Triosephosphate isomerase                                                                                                                                                                                                                  SCOP domains
               CATH domains 1mo0B00 B:3-247 Aldolase class I                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) --TIM-1mo0B01 B:5-243                                                                                                                                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) --TIM-1mo0B02 B:5-243                                                                                                                                                                                                                            ---- Pfam domains (2)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh...eeeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhh......eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......hhhhhh......eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: B:4-245 UniProt: 4-245                                                                                                                                                                                                                -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mo0 B   3 RKFFVGGNWKMNGDYASVDGIVTFLNASADNSSVDVVVAPPAPYLAYAKSKLKAGVLVAAQNCYKVPKGAFTGEISPAMIKDLGLEWVILGHSERRHVFGESDALIAEKTVHALEAGIKVVFCIGEKLEEREAGHTKDVNFRQLQAIVDKGVSWENIVIAYEPVWAIGTGKTASGEQAQEVHEWIRAFLKEKVSPAVADATRIIYGGSVTADNAAELGKKPDIDGFLVGGASLKPDFVKIINARS 247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Triosephosphate isomerase (TIM) (148)

Family: Triosephosphate isomerase (TIM) (128)

Protein domain: Triosephosphate isomerase (126)

Nematode (Caenorhabditis elegans) [TaxId: 6239] (1)

1a	d1mo0a_	A:
1b	d1mo0b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Caenorhabditis elegans. Organism_taxid: 6239. (1)

1a	1mo0A00	A:-7-249
1b	1mo0B00	B:3-247

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: TIM (80)

Caenorhabditis elegans (1)

1a	TIM-1mo0B01	B:5-243
1b	TIM-1mo0B02	B:5-243

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TPIS_CAEEL | Q10657)

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:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0008340	determination of adult lifespan	The control of viability and duration in the adult phase of the life-cycle.
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0046166	glyceraldehyde-3-phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
	GO:0019563	glycerol catabolic process	The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0030016	myofibril	The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.

Asymmetric/Biological Unit
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1lpl	RELATED ID: AAA79846 RELATED DB: TARGETDB

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

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