1USL - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE ISOMERASE, RPIB, RV2465C, COMPLEXED WITH PHOSPHATE.

Authors :   A. K. Roos, C. E. Andersson, T. Unge, T. A. Jones, S. L. Mowbray

Date :   25 Nov 03 (Deposition) - 02 Jan 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E  (2x)

Keywords :   Isomerase, Phosphopentose Isomerase B, Pentose Phosphate Pathway, Rv2465C, Phosphoriboisomerase B, Structural Proteomics In Europe, Spine, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Roos, C. E. Andersson, T. Bergfors, M. Jacobsson, A. Karlen, T. Unge, T. A. Jones, S. L. Mowbray
Mycobacterium Tuberculosis Ribose-5-Phosphate Isomerase Has A Known Fold, But A Novel Active Site
J. Mol. Biol. V. 335 799 2004
PubMed-ID: 14687575 | Reference-DOI: 10.1016/J.JMB.2003.11.021

Molecule 1 - RIBOSE 5-PHOSPHATE ISOMERASE B
	Chains	:	A, B, C, D, E
	EC Number	:	5.3.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCR_T7
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (2x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	PO4	5	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:137 , ARG A:141 , HOH A:2110 , HOH A:2111 , HOH A:2112 , HIS B:12 , ARG B:113	BINDING SITE FOR RESIDUE PO4 A1159
2	AC2	SOFTWARE	HIS A:12 , ALA A:13 , HOH A:2007 , ARG B:137 , HIS B:138 , ARG B:141 , HOH B:2114 , HOH B:2115 , HOH B:2116	BINDING SITE FOR RESIDUE PO4 B1159
3	AC3	SOFTWARE	ARG C:137 , ARG C:141 , HOH C:2110 , HOH C:2111 , HIS D:12 , HOH D:2005	BINDING SITE FOR RESIDUE PO4 C1161
4	AC4	SOFTWARE	HIS C:12 , HOH C:2004 , ARG D:137 , HIS D:138 , ARG D:141 , HOH D:2137 , HOH D:2138 , HOH D:2139	BINDING SITE FOR RESIDUE PO4 D1159
5	AC5	SOFTWARE	HIS E:12 , ARG E:137 , HIS E:138 , ARG E:141 , HOH E:2100 , HOH E:2101	BINDING SITE FOR RESIDUE PO4 E1159

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

Asymmetric Unit

No.	Residues
1	Gly A:36	-	Ala A:37
2	Gly B:36	-	Ala B:37
3	Gly C:36	-	Ala C:37
4	Gly D:36	-	Ala D:37
5	Gly E:36	-	Ala E:37

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

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

(no "Exon" information available for 1USL)

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:157
 aligned with RPIB_MYCTU | P9WKD7 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       
           RPIB_MYCTU     3 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPG 159
               SCOP domains d1usla_ A: Alternate ribose 5-phosphate isomerase B, RpiB                                                                                                     SCOP domains
               CATH domains 1uslA00 A:3-159  [code=3.40.1400.10, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhh....eeeeee..hhhhhhhhh.....eeeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1usl A   3 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPG 159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with RPIB_MYCTU | P9WKD7 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       
           RPIB_MYCTU     3 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPG 159
               SCOP domains d1uslb_ B: Alternate ribose 5-phosphate isomerase B, RpiB                                                                                                     SCOP domains
               CATH domains 1uslB00 B:3-159  [code=3.40.1400.10, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhh....eeeeee..hhhhhhhhh.....eeeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1usl B   3 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPG 159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain C from PDB  Type:PROTEIN  Length:159
 aligned with RPIB_MYCTU | P9WKD7 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152         
           RPIB_MYCTU     3 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPGAP 161
               SCOP domains d1uslc_ C: Alternate ribose 5-phosphate isomerase B, RpiB                                                                                                       SCOP domains
               CATH domains 1uslC00 C:3-161  [code=3.40.1400.10, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhh....eeeeee..hhhhhhhhh.....eeeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1usl C   3 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPGAP 161
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain D from PDB  Type:PROTEIN  Length:158
 aligned with RPIB_MYCTU | P9WKD7 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           RPIB_MYCTU     2 SGMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPG 159
               SCOP domains d1usld_ D: Alternate ribose 5-phosphate isomerase B, RpiB                                                                                                      SCOP domains
               CATH domains 1uslD00 D:2-159  [code=3.40.1400.10, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhh....eeeeee..hhhhhhhhh.....eeeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1usl D   2 SGMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPG 159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain E from PDB  Type:PROTEIN  Length:157
 aligned with RPIB_MYCTU | P9WKD7 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       
           RPIB_MYCTU     3 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPG 159
               SCOP domains d1usle_ E: Alternate ribose 5-phosphate isomerase B, RpiB                                                                                                     SCOP domains
               CATH domains 1uslE00 E:3-159  [code=3.40.1400.10, no name defined]                                                                                                         CATH domains
           Pfam domains (1) --LacAB_rpiB-1uslE01 E:5-146                                                                                                                    ------------- Pfam domains (1)
           Pfam domains (2) --LacAB_rpiB-1uslE02 E:5-146                                                                                                                    ------------- Pfam domains (2)
           Pfam domains (3) --LacAB_rpiB-1uslE03 E:5-146                                                                                                                    ------------- Pfam domains (3)
           Pfam domains (4) --LacAB_rpiB-1uslE04 E:5-146                                                                                                                    ------------- Pfam domains (4)
           Pfam domains (5) --LacAB_rpiB-1uslE05 E:5-146                                                                                                                    ------------- Pfam domains (5)
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhh....eeeeee..hhhhhhhhh.....eeeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1usl E   3 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPG 159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

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: Ribose/Galactose isomerase RpiB/AlsB (27)

Superfamily: Ribose/Galactose isomerase RpiB/AlsB (27)

Family: Ribose/Galactose isomerase RpiB/AlsB (12)

Protein domain: Alternate ribose 5-phosphate isomerase B, RpiB (7)

Mycobacterium tuberculosis [TaxId: 1773] (6)

1a	d1usla_	A:
1b	d1uslb_	B:
1c	d1uslc_	C:
1d	d1usld_	D:
1e	d1usle_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Ribose 5-phosphate Isomerase B; Chain: A, (13)

Homologous Superfamily: [code=3.40.1400.10, no name defined] (13)

Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. (6)

1a	1uslC00	C:3-161
1b	1uslA00	A:3-159
1c	1uslB00	B:3-159
1d	1uslE00	E:3-159
1e	1uslD00	D:2-159

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: LacAB_rpiB (12)

Mycobacterium tuberculosis (3)

1a	LacAB_rpiB-1uslE01	E:5-146
1b	LacAB_rpiB-1uslE02	E:5-146
1c	LacAB_rpiB-1uslE03	E:5-146
1d	LacAB_rpiB-1uslE04	E:5-146
1e	LacAB_rpiB-1uslE05	E:5-146

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (RPIB_MYCTU | P9WKD7)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004751	ribose-5-phosphate isomerase activity	Catalysis of the reaction: D-ribose 5-phosphate = D-ribulose 5-phosphate.
biological process
	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.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:36 - Ala A:37	[ RasMol ]
		Gly B:36 - Ala B:37	[ RasMol ]
		Gly C:36 - Ala C:37	[ RasMol ]
		Gly D:36 - Ala D:37	[ RasMol ]
		Gly E:36 - Ala E:37	[ RasMol ]

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	RPIB_MYCTU \| P9WKD7	:	2bes 2bet 2vvo 2vvp 2vvq

(no "Related Entries Specified in the PDB File" available for 1USL)

Description

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