1R2S - JenaLib

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Title :   CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE

Authors :   R. Aparicio, S. T. Ferreira, I. Polikarpov

Date :   29 Sep 03 (Deposition) - 23 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Tim; Closed Loop Conformation In The Ligand-Free State; Conformational Heterogeneity; Tim-Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Aparicio, S. T. Ferreira, I. Polikarpov
Closed Conformation Of The Active Site Loop Of Rabbit Muscl Triosephosphate Isomerase In The Absence Of Substrate: Evidence Of Conformational Heterogeneity.
J. Mol. Biol. V. 334 1023 2003
PubMed-ID: 14643664 | Reference-DOI: 10.1016/J.JMB.2003.10.022
(for further references see the PDB file header)

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.3.1.1
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	TIM
	Tissue	:	MUSCLE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1R2S)

(no "Site" information available for 1R2S)

(no "SS Bond" information available for 1R2S)

(no "Cis Peptide Bond" information available for 1R2S)

(no "SAP(SNP)/Variant" information available for 1R2S)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_RABIT	5-246	4	A:5-246 B:5-246 C:5-246 D:5-246
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_RABIT	163-173	4	A:163-173 B:163-173 C:163-173 D:163-173

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_RABIT	5-246	2	A:5-246 B:5-246 - -
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_RABIT	163-173	2	A:163-173 B:163-173 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_RABIT	5-246	2	- - C:5-246 D:5-246
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_RABIT	163-173	2	- - C:163-173 D:163-173

(no "Exon" information available for 1R2S)

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:247
 aligned with TPIS_RABIT | P00939 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    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_RABIT     2 PSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
               SCOP domains d1r2sa_ A: Triosephosphate isomerase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1r2sA00 A:2-248 Aldolase class I                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh...hhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......hhhhhhh.....eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TIM_2  PDB: A:5-246 UniProt: 5-246                                                                                                                                                                                                                -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r2s A   2 PSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
                                    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:246
 aligned with TPIS_RABIT | P00939 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    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_RABIT     3 SRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
               SCOP domains d1r2sb_ B: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1r2sB00 B:3-248 Aldolase class I                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh...hhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......hhhhhhh.....eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --TIM_2  PDB: B:5-246 UniProt: 5-246                                                                                                                                                                                                                -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r2s B   3 SRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
                                    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 C from PDB  Type:PROTEIN  Length:247
 aligned with TPIS_RABIT | P00939 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    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_RABIT     2 PSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
               SCOP domains d1r2sc_ C: Triosephosphate isomerase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1r2sC00 C:2-248 Aldolase class I                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh...hhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......hhhhhhh.....eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TIM_2  PDB: C:5-246 UniProt: 5-246                                                                                                                                                                                                                -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r2s C   2 PSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
                                    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 D from PDB  Type:PROTEIN  Length:247
 aligned with TPIS_RABIT | P00939 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    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_RABIT     2 PSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
               SCOP domains d1r2sd_ D: Triosephosphate isomerase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1r2sD00 D:2-248 Aldolase class I                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh...hhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhh.....eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TIM_2  PDB: D:5-246 UniProt: 5-246                                                                                                                                                                                                                -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r2s D   2 PSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ 248
                                    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 '\|'

Asymmetric 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)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (4)

1a	d1r2sa_	A:
1b	d1r2sc_	C:
1c	d1r2sd_	D:
1d	d1r2sb_	B:

Asymmetric 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)

Rabbit (Oryctolagus cuniculus) (27)

1a	1r2sA00	A:2-248
1b	1r2sC00	C:2-248
1c	1r2sD00	D:2-248
1d	1r2sB00	B:3-248

(no "Pfam Domain" information available for 1R2S)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TPIS_RABIT | P00939)

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.

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	1r2s
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