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(-) Description

Title :  CRYSTAL STRUCTURE OF THE H99N MUTANT OF RIBOSE-5-PHOSPHATE ISOMERASE B FROM E. COLI SOAKED WITH RIBOSE 5-PHOSPHATE
 
Authors :  A. K. Roos, S. L. Mowbray
Date :  11 Jun 08  (Deposition) - 08 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Rpib, Isomerase, Carbohydrate Metabolism, Pentose Phosphate Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Roos, S. Mariano, E. Kowalinski, L. Salmon, S. L. Mowbray
D-Ribose-5-Phosphate Isomerase B From Escherichia Coli Is Also A Functional D-Allose-6-Phosphate Isomerase, While The Mycobacterium Tuberculosis Enzyme Is Not.
J. Mol. Biol. V. 382 667 2008
PubMed-ID: 18640127  |  Reference-DOI: 10.1016/J.JMB.2008.06.090

(-) Compounds

Molecule 1 - RIBOSE-5-PHOSPHATE ISOMERASE B
    Chains: A, B, C, D, E, F
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD/TOPO
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: PHOSPHORIBOISOMERASE B

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2VVR)

(-) Sites  (0, 0)

(no "Site" information available for 2VVR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VVR)

(-) Cis Peptide Bonds  (6, 6)

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
5Gly E:34 -Thr E:35
6Gly F:34 -Thr F:35

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VVR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VVR)

(-) Exons   (0, 0)

(no "Exon" information available for 2VVR)

(-) 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:147
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
           RPIB_ECOLI     1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQR 147
               SCOP domains d2vvra_ A: automated matches                                                                                                                        SCOP domains
               CATH domains 2vvrA00 A:1-147  [code=3.40.1400.10, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvr A   1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQNNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQR 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           RPIB_ECOLI     1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
               SCOP domains d2vvrb_ B: automated matches                                                                                                                       SCOP domains
               CATH domains 2vvrB00 B:1-146  [code=3.40.1400.10, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvr B   1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQNNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      


Chain C from PDB  Type:PROTEIN  Length:147
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
           RPIB_ECOLI     1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQR 147
               SCOP domains d2vvrc_ C: automated matches                                                                                                                        SCOP domains
               CATH domains 2vvrC00 C:1-147  [code=3.40.1400.10, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvr C   1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQNNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQR 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain D from PDB  Type:PROTEIN  Length:146
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           RPIB_ECOLI     1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
               SCOP domains d2vvrd_ D: automated matches                                                                                                                       SCOP domains
               CATH domains 2vvrD00 D:1-146  [code=3.40.1400.10, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvr D   1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQNNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      


Chain E from PDB  Type:PROTEIN  Length:147
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
           RPIB_ECOLI     1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQR 147
               SCOP domains d2vvre_ E: automated matches                                                                                                                        SCOP domains
               CATH domains 2vvrE00 E:1-147  [code=3.40.1400.10, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvr E   1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQNNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQR 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain F from PDB  Type:PROTEIN  Length:146
 aligned with RPIB_ECOLI | P37351 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           RPIB_ECOLI     1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
               SCOP domains d2vvrf_ F: automated matches                                                                                                                       SCOP domains
               CATH domains 2vvrF00 F:1-146  [code=3.40.1400.10, no name defined]                                                                                              CATH domains
           Pfam domains (1) --LacAB_rpiB-2vvrF01 F:3-142                                                                                                                  ---- Pfam domains (1)
           Pfam domains (2) --LacAB_rpiB-2vvrF02 F:3-142                                                                                                                  ---- Pfam domains (2)
           Pfam domains (3) --LacAB_rpiB-2vvrF03 F:3-142                                                                                                                  ---- Pfam domains (3)
           Pfam domains (4) --LacAB_rpiB-2vvrF04 F:3-142                                                                                                                  ---- Pfam domains (4)
           Pfam domains (5) --LacAB_rpiB-2vvrF05 F:3-142                                                                                                                  ---- Pfam domains (5)
           Pfam domains (6) --LacAB_rpiB-2vvrF06 F:3-142                                                                                                                  ---- Pfam domains (6)
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvr F   1 MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQNNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQ 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

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,E,F   (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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  Cis Peptide Bonds
    Gly A:34 - Thr A:35   [ RasMol ]  
    Gly B:34 - Thr B:35   [ RasMol ]  
    Gly C:34 - Thr C:35   [ RasMol ]  
    Gly D:34 - Thr D:35   [ RasMol ]  
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  2vvr
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  RPIB_ECOLI | P37351
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  5.3.1.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPIB_ECOLI | P37351: 1nn4

(-) Related Entries Specified in the PDB File

1nn4 STRUCTURAL GENOMICS, RPIB/ALSB
2vvo CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE ISOMERASE B IN COMPLEX WITH ALPHA ALLOSE 6-PHOSPHATE
2vvp CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE ISOMERASE B IN COMPLEX WITH ITS SUBSTRATES RIBOSE 5-PHOSPHATE AND RIBULOSE 5-PHOSPHATE
2vvq CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE ISOMERASE B IN COMPLEX WITH THE INHIBITOR 5-DEOXY-5-PHOSPHO-D- RIBONATE