2IXL - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   RMLC S. SUIS WITH DTDP-RHAMNOSE

Authors :   C. Dong, J. H. Naismith

Date :   08 Jul 06 (Deposition) - 26 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Epimerise, Epimerase, Isomerase, Epimerize (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Dong, L. L. Major, V. Srikannathasan, J. C. Errey, M. F. Giraud, J. S. Lam, M. Graninger, P. Messner, M. R. Mcneil, R. A. Field, C. Whitfield, J. H. Naismith
Rmlc, A C3' And C5' Carbohydrate Epimerase, Appears To Operate Via An Intermediate With An Unusual Twist Boat Conformation.
J. Mol. Biol. V. 365 146 2007
PubMed-ID: 17046787 | Reference-DOI: 10.1016/J.JMB.2006.09.063

Molecule 1 - DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.1.3.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	STREPTOCOCCUS SUIS
	Organism Taxid	:	1307
	Synonym	:	RMLC

		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)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	NI	2	Ligand/Ion	NICKEL (II) ION
2	TRH	4	Ligand/Ion	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	TRH	2	Ligand/Ion	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	TRH	2	Ligand/Ion	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:52 , HOH A:2135 , HOH A:2142 , GLU C:52	BINDING SITE FOR RESIDUE NI A1199
2	AC2	SOFTWARE	GLU A:52 , HOH A:2135 , HOH A:2142 , GLU C:52	BINDING SITE FOR RESIDUE NI C1199
3	AC3	SOFTWARE	GLN A:61 , ARG A:73 , HIS A:76 , GLU A:78 , LYS A:82 , ASN A:127 , TYR A:140 , TRP A:146 , HOH A:2179 , HOH A:2320 , HOH A:2356 , HOH A:2357 , HOH A:2358 , HOH A:2359 , HOH A:2360 , HOH A:2361 , HOH A:2363 , HOH A:2364 , HOH A:2365 , ARG B:33 , PHE B:36 , GLU B:38	BINDING SITE FOR RESIDUE TRH A1198
4	AC4	SOFTWARE	ARG A:33 , PHE A:36 , GLU A:38 , GLN B:61 , ARG B:73 , HIS B:76 , GLU B:78 , LYS B:82 , ASN B:127 , TYR B:140 , TRP B:146 , HOH B:2197 , HOH B:2361 , HOH B:2362 , HOH B:2363 , HOH B:2364 , HOH B:2365 , HOH B:2366 , HOH B:2367 , HOH B:2369 , HOH B:2370	BINDING SITE FOR RESIDUE TRH B1198
5	AC5	SOFTWARE	GLN C:61 , HIS C:76 , GLU C:78 , LYS C:82 , ASN C:127 , TRP C:146 , HOH C:2352 , HOH C:2353 , HOH C:2354 , HOH C:2355 , HOH C:2357 , HOH C:2358 , HOH C:2359 , GLU D:38 , GLU D:178 , HOH D:2344	BINDING SITE FOR RESIDUE TRH C1198
6	AC6	SOFTWARE	HIS C:29 , ARG C:33 , PHE C:36 , GLU C:38 , GLN D:61 , ARG D:73 , HIS D:76 , GLU D:78 , LYS D:82 , ASN D:127 , TYR D:140 , TRP D:146 , HOH D:2195 , HOH D:2265 , HOH D:2336 , HOH D:2372 , HOH D:2373 , HOH D:2374 , HOH D:2375 , HOH D:2376 , HOH D:2378 , HOH D:2379 , HOH D:2381	BINDING SITE FOR RESIDUE TRH D1198

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

Asymmetric Unit

No.	Residues
1	Gly A:74	-	Leu A:75
2	Gly B:74	-	Leu B:75
3	Gly C:74	-	Leu C:75
4	Gly D:74	-	Leu D:75

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

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

(no "Exon" information available for 2IXL)

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:196
 aligned with Q8GIQ0_STRSU | Q8GIQ0 from UniProtKB/TrEMBL  Length:197

    Alignment length:196
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191      
         Q8GIQ0_STRSU     2 TENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
               SCOP domains d2ixla_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                 SCOP domains
               CATH domains 2ixlA00 A:2-197 Jelly Rolls                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.......eeee..eeee..eeeeeeeehhhhhhhh.hhhhhh....eeeeeeee...eeeeee....eeeee.....eeeeeee.........eeeeee...eeeee...eeeeeee...eeeeeeee....hhhhhhhhee....................hhhhhhh.hhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ixl A   2 TENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with Q8GIQ0_STRSU | Q8GIQ0 from UniProtKB/TrEMBL  Length:197

    Alignment length:195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     
         Q8GIQ0_STRSU     3 ENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
               SCOP domains d2ixlb_ B: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                SCOP domains
               CATH domains 2ixlB00 B:3-197 Jelly Rolls                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.......eeee..eeee..eeeeeeeehhhhhhhh.hhhhhh....eeeeeeee...eeeeee....eeeee.....eeeeeee.........eeeeee...eeeee...eeeeeee...eeeeeeee....hhhhhhhhee....................hhhhhh..hhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ixl B   3 ENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain C from PDB  Type:PROTEIN  Length:197
 aligned with Q8GIQ0_STRSU | Q8GIQ0 from UniProtKB/TrEMBL  Length:197

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
         Q8GIQ0_STRSU     1 MTENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
               SCOP domains d2ixlc_ C: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                  SCOP domains
               CATH domains 2ixlC00 C:1-197 Jelly Rolls                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee.......eeee..eeee..eeeeeeeehhhhhhhh.hhhhhh....eeeeeeee...eeeeee....eeeee.....eeeeeee.........eeeeee...eeeee...eeeeeee...eeeeeeee....hhhhhhhhee.............hhhhh..hhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ixl C   1 MTENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain D from PDB  Type:PROTEIN  Length:196
 aligned with Q8GIQ0_STRSU | Q8GIQ0 from UniProtKB/TrEMBL  Length:197

    Alignment length:196
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191      
         Q8GIQ0_STRSU     2 TENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
               SCOP domains d2ixld_ D: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                 SCOP domains
               CATH domains 2ixlD00 D:2-197 Jelly Rolls                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.......eeee..eeee..eeeeeeeehhhhhhhh.hhhhhh....eeeeeeee...eeeeee....eeeee.....eeeeeee.........eeeeee...eeeee...eeeeeee...eeeeeeee....hhhhhhhhee....................hhhhhhh.hhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ixl D   2 TENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: RmlC-like cupins (220)

Family: dTDP-sugar isomerase (26)

Protein domain: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC (18)

Streptococcus suis [TaxId: 1307] (4)

1a	d2ixla_	A:
1b	d2ixlb_	B:
1c	d2ixlc_	C:
1d	d2ixld_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

Streptococcus suis. Organism_taxid: 1307. (1)

1a	2ixlB00	B:3-197
1b	2ixlA00	A:2-197
1c	2ixlD00	D:2-197
1d	2ixlC00	C:1-197

(no "Pfam Domain" information available for 2IXL)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q8GIQ0_STRSU | Q8GIQ0)

molecular function
	GO:0008830		dTDP-4-dehydrorhamnose 3,5-epimerase activity		Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:74 - Leu A:75	[ RasMol ]
		Gly B:74 - Leu B:75	[ RasMol ]
		Gly C:74 - Leu C:75	[ RasMol ]
		Gly D:74 - Leu D:75	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	2ixl
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	5.1.3.13
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UniProtKB/TrEMBL
	Q8GIQ0_STRSU \| Q8GIQ0	:	1nxm 1nyw 1nzc

1nxm	THE HIGH RESOLUTION STRUCTURES OF RMLC FROM STREPTOCOCCUSSUIS
1nyw	THE HIGH RESOLUTION STRUCTURES OF RMLC FROM STREPTOCCUSSUIS IN COMPLEX WITH DTDP-D- GLUCOSE
1nzc	THE HIGH RESOLUTION STRUCTURES OF RMLC FROM STREPTOCOCCUSSUIS IN COMPLEX WITH DTDP-D- XYLOSE

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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