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(-) Description

Title :  STRUCTURAL GENOMICS, RPIB/ALSB
 
Authors :  R. G. Zhang, C. E. Andersson, S. L. Mowbray, A. Savchenko, T. Skarina, E. Evdokimova, S. L. Beasley, C. Arrowsmith, A. M. Edwards, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  12 Jan 03  (Deposition) - 29 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Structural Genomics, Alpha/Beta/Alpha Sandwich, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. G. Zhang, C. E. Andersson, T. Skarina, E. Evdokimova, A. M. Edwards, A. Joachimiak, A. Savchenko, S. L. Mowbray
The 2. 2 A Resolution Structure Of Rpib/Alsb From Escherichia Coli Illustrates A New Approach To The Ribose-5-Phosphate Isomerase Reaction.
J. Mol. Biol. V. 332 1083 2003
PubMed-ID: 14499611  |  Reference-DOI: 10.1016/J.JMB.2003.08.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSE 5-PHOSPHATE ISOMERASE B
    Chains: A, B, C, D
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPIB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PHOSPHORIBOISOMERASE B, RPIB/ALSB

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1NN4)

(-) Sites  (0, 0)

(no "Site" information available for 1NN4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NN4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:34 -Thr A:35
2Gly B:34 -Thr B:35
3Gly C:34 -Thr C:35
4Gly D:34 -Thr D:35

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NN4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NN4)

(-) Exons   (0, 0)

(no "Exon" information available for 1NN4)

(-) Sequences/Alignments

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:159
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:159
                                         1                                                                                                                                                 
                                     -   |     7        17        27        37        47        57        67        77        87        97       107       117       127       137         
           RPIB_ECOLI     - -------------MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
               SCOP domains d1nn4a_ A: Alternate ribose 5-phosphate isomerase B, RpiB                                                                                                       SCOP domains
               CATH domains 1nn4A00 A:-12-146  [code=3.40.1400.10, no name defined]                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......eeeeee...hhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nn4 A -12 HHHSSGLTPRGSQMKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
                                    -3         7        17        27        37        47        57        67        77        87        97       107       117       127       137         


Chain B from PDB  Type:PROTEIN  Length:158
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:158
                                        1                                                                                                                                                 
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138        
           RPIB_ECOLI     - ------------MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
               SCOP domains d1nn4b_ B: Alternate ribose 5-phosphate isomerase B, RpiB                                                                                                      SCOP domains
               CATH domains 1nn4B00 B:-11-146  [code=3.40.1400.10, no name defined]                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......eeeeee...hhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nn4 B -11 HHSSGLTPRGSQMKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
                                    -2         8        18        28        38        48        58        68        78        88        98       108       118       128       138        


Chain C from PDB  Type:PROTEIN  Length:159
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:159
                                         1                                                                                                                                                 
                                     -   |     7        17        27        37        47        57        67        77        87        97       107       117       127       137         
           RPIB_ECOLI     - -------------MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
               SCOP domains d1nn4c_ C: Alternate ribose 5-phosphate isomerase B, RpiB                                                                                                       SCOP domains
               CATH domains 1nn4C00 C:-12-146  [code=3.40.1400.10, no name defined]                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......eeeeee...hhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhh......eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.....hhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nn4 C -12 HHHSSGLTPRGSQMKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
                                    -3         7        17        27        37        47        57        67        77        87        97       107       117       127       137         


Chain D from PDB  Type:PROTEIN  Length:159
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:159
                                        1                                                                                                                                                  
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138         
           RPIB_ECOLI     - ------------MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQR 147
               SCOP domains d1nn4d_ D: Alternate ribose 5-phosphate isomerase B, RpiB                                                                                                       SCOP domains
               CATH domains 1nn4D00 D:-11-147  [code=3.40.1400.10, no name defined]                                                                                                         CATH domains
           Pfam domains (1) --------------LacAB_rpiB-1nn4D01 D:3-142                                                                                                                  ----- Pfam domains (1)
           Pfam domains (2) --------------LacAB_rpiB-1nn4D02 D:3-142                                                                                                                  ----- Pfam domains (2)
           Pfam domains (3) --------------LacAB_rpiB-1nn4D03 D:3-142                                                                                                                  ----- Pfam domains (3)
           Pfam domains (4) --------------LacAB_rpiB-1nn4D04 D:3-142                                                                                                                  ----- Pfam domains (4)
         Sec.struct. author .....eee......eeeeee...hhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nn4 D -11 HHSSGLTPRGSQMKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQR 147
                                    -2         8        18        28        38        48        58        68        78        88        98       108       118       128       138
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: LacAB_rpiB] (12)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RPIB_ECOLI | P37351)
molecular function
    GO:0008786    allose 6-phosphate isomerase activity    Catalysis of the reaction: D-allose-6-phosphate = D-allulose-6-phosphate.
    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:0019316    D-allose catabolic process    The chemical reactions and pathways resulting in the breakdown of D-allose, the D-enantiomer of allo-hexose, an aldohexose similar to glucose.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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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 Related Entries

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

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        RPIB_ECOLI | P37351: 2vvr

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