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Title :   STRUCTURE OF ESCHERICHIA COLI RIBOSE-5-PHOSPHATE ISOMERASE, RPIA, COMPLEXED WITH ARABINOSE-5-PHOSPHATE.

Authors :   R. -G. Zhang, C. E. Andersson, A. Savchenko, T. Skarina, E. Evdokimova, S. Beasley, C. H. Arrowsmith, A. M. Edwards, A. Joachimiak, S. L. Mowbr Midwest Center For Structural Genomics (Mcsg)

Date :   26 Nov 02 (Deposition) - 24 Jan 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

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

Keywords :   Isomerase, Ribose Phosphate Isomerase, Rpia, Psi, Protein Structure Initiative, Mcsg, Midwest Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. -G. Zhang, C. E. Andersson, A. Savchenko, T. Skarina, E. Evdokimova S. Beasley, C. H. Arrowsmith, A. M. Edwards, A. Joachimiak, S. L. Mowbray
Structure Of Escherichia Coli Ribose-5-Phosphate Isomerase: A Ubiquitous Enzyme Of The Pentose Phosphate Pathway And The Calvin Cycle
Structure V. 11 31 2003
PubMed-ID: 12517338 | Reference-DOI: 10.1016/S0969-2126(02)00933-4
(for further references see the PDB file header)

Molecule 1 - RIBOSE 5-PHOSPHATE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PHOSPHORIBOISOMERASE A, RPIA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 13)

No.	Name	Count	Type	Full Name
1	ABF	2	Ligand/Ion	BETA-D-ARABINOFURANOSE-5'-PHOSPHATE
2	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:28 , SER A:30 , THR A:31 , ASP A:81 , ASP A:84 , LYS A:94 , GLY A:95 , GLY A:96 , GLY A:97 , GLU A:103 , LYS A:121 , HOH A:2020 , HOH A:2068 , HOH A:2069	BINDING SITE FOR RESIDUE ABF A1269
2	AC2	SOFTWARE	THR B:28 , GLY B:29 , SER B:30 , THR B:31 , ASP B:81 , GLY B:82 , ASP B:84 , LYS B:94 , GLY B:95 , GLY B:96 , GLY B:97 , GLU B:103 , LYS B:121 , HOH B:2020 , HOH B:2037 , HOH B:2088 , HOH B:2089 , HOH B:2090	BINDING SITE FOR RESIDUE ABF B1269

(no "SS Bond" information available for 1O8B)

(no "Cis Peptide Bond" information available for 1O8B)

(no "SAP(SNP)/Variant" information available for 1O8B)

(no "PROSITE Motif" information available for 1O8B)

(no "Exon" information available for 1O8B)

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:168
 aligned with RPIA_ECOLI | P0A7Z0 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:196
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
           RPIA_ECOLI    23 IVGVGTGSTAAHFIDALGTMKGQIEGAVSSSDASTEKLKSLGIHVFDLNEVDSLGIYVDGADEINGHMQMIKGGGAALTREKIIASVAEKFICIADASKQVDILGKFPLPVEVIPMARSAVARQLVKLGGRPEYRQGVVTDNGNVILDVHGMEILDPIAMENAINAIPGVVTVGLFANRGADVALIGTPDGVKTIV 218
               SCOP domains d1o8ba1 A               :23-126,A            :199-218 D-ribose-5-phosphate  isomerase (RpiA), catalytic d1o8ba2 A:127-198 D-ribose-5-phosphate isomerase (RpiA), lid domain     d1o8ba1              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------1o8bA02 A:125-196  [code=3.30.70.260, no name defined]                  ---------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....---------------.eeeee...------------.hhhhh...eeeee...ee...eeeee...-.hhhhhhhhhh..eeeee....eee.......eeeee...hhhhhhhhhhhh..eeee..........eeeeee......hhhhhhhhhh...eeeeeee......eeeeee.eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o8b A  23 IVGVGTGST---------------EGAVSSSDA------------FDLNEVDSLGIYVDGADEINGHmQmIKGGG-ALTREKIIASVAEKFICIADASKQVDILGKFPLPVEVIPmARSAVARQLVKLGGRPEYRQGVVTDNGNVILDVHGmEILDPIAmENAINAIPGVVTVGLFANRGADVALIGTPDGVKTIV 218
                                    |-         -    |   52  |      -     |  72        82       |92    | |102       112       122       132     | 142       152       162       172 |     182       192       202       212      
                                   31              47      55           68                    90-MSE 97 |                                    138-MSE                             174-MSE 182-MSE                                
                                                                                                92-MSE 99

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with RPIA_ECOLI | P0A7Z0 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
           RPIA_ECOLI     2 TQDELKKAVGWAALQYVQPGTIVGVGTGSTAAHFIDALGTMKGQIEGAVSSSDASTEKLKSLGIHVFDLNEVDSLGIYVDGADEINGHMQMIKGGGAALTREKIIASVAEKFICIADASKQVDILGKFPLPVEVIPMARSAVARQLVKLGGRPEYRQGVVTDNGNVILDVHGMEILDPIAMENAINAIPGVVTVGLFANRGADVALIGTPDGVKTIV 218
               SCOP domains d1o8bb1 B:2-126,    B:199-218 D-ribose-5-phosphate isomerase (RpiA), catalytic domain                                        d1o8bb2 B:127-198 D-ribose-5-phosphate isomerase (RpiA), lid domain     d1o8bb1              SCOP domains
               CATH domains 1o8bB01 B:2-124,    B:197-218  [code=3.40.50.1360, no name defined]                                                        1o8bB02 B:125-196  [code=3.30.70.260, no name defined]                  1o8bB01                CATH domains
           Pfam domains (1) ----------------    -------------------------Rib_5-P_isom_A-1o8bB01 B:47-215                                                                                                                                          --- Pfam domains (1)
           Pfam domains (2) ----------------    -------------------------Rib_5-P_isom_A-1o8bB02 B:47-215                                                                                                                                          --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhh----.eeee..hhhhhhhhhhhhh......eeeee.hhhhhhhhhh..eeehhhhh..eeeeee........eeee....-.hhhhhhhhhh..eeeee....eee.......eeeee...hhhhhhhhhhhh..eeee..........eeeeee......hhhhhhhhhh...eeeeeee......eeeeee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o8b B   2 TQDELKKAVGWAALQY----TIVGVGTGSTAAHFIDALGTmKGQIEGAVSSSDASTEKLKSLGIHVFDLNEVDSLGIYVDGADEINGHmQmIKGGG-ALTREKIIASVAEKFICIADASKQVDILGKFPLPVEVIPmARSAVARQLVKLGGRPEYRQGVVTDNGNVILDVHGmEILDPIAmENAINAIPGVVTVGLFANRGADVALIGTPDGVKTIV 218
                                    11     |   -|       31        41|       51        61        71        81        91|    | 101       111       121       131      |141       151       161       171  |    181|      191       201       211       
                                          17   22                  42-MSE                                          90-MSE 97 |                                    138-MSE                             174-MSE 182-MSE                                
                                                                                                                     92-MSE 99

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.260, no name defined] (34)

Escherichia coli. Organism_taxid: 562. (2)

1a	1o8bA02	A:125-196
1b	1o8bB02	B:125-196

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1360, no name defined] (40)

Escherichia coli. Organism_taxid: 562. (10)

1o8bB01

B:2-124,B:197-218

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ISOCOT_Fold (53)

Family: Rib_5-P_isom_A (10)

Escherichia coli (strain K12) (3)

1a	Rib_5-P_isom_A-1o8bB01	B:47-215
1b	Rib_5-P_isom_A-1o8bB02	B:47-215

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RPIA_ECOLI | P0A7Z0)

molecular function
	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:0004751	ribose-5-phosphate isomerase activity	Catalysis of the reaction: D-ribose 5-phosphate = D-ribulose 5-phosphate.
biological process
	GO:0006014	D-ribose metabolic process	The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
	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.
	GO:0009052	pentose-phosphate shunt, non-oxidative branch	The branch of the pentose-phosphate shunt which does not involve oxidation reactions. It comprises a series of sugar phosphate interconversions, starting with ribulose 5-P and producing fructose 6-P and glyceraldehyde 3-P.
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.

Asymmetric/Biological Unit
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	RPIA_ECOLI \| P0A7Z0	:	1ks2 1lkz

1lkz	CRYSTAL STRUCTURE OF D-RIBOSE-5-PHOSPHATE ISOMERASE (RPIA)FROM ESCHERICHIA COLI. RELATED ID: APC065 RELATED DB: TARGETDB

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