1NZC - JenaLib

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Title :   THE HIGH RESOLUTION STRUCTURES OF RMLC FROM STREPTOCOCCUS SUIS IN COMPLEX WITH DTDP-D-XYLOSE

Authors :   C. Dong, L. L. Major, A. Allen, W. Blankenfeldt, D. Maskell, J. H. Naismith

Date :   17 Feb 03 (Deposition) - 24 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Jelly Roll-Like Structure; Beta Sheet, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Dong, L. L. Major, A. Allen, W. Blankenfeldt, D. Maskell, J. H. Naismith
High-Resolution Structures Of Rmlc From Streptococcus Suis In Complex With Substrate Analogs Locate The Active Site Of This Class Of Enzyme
Structure V. 11 715 2003
PubMed-ID: 12791259 | Reference-DOI: 10.1016/S0969-2126(03)00098-4
(for further references see the PDB file header)

Molecule 1 - DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.1.3.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RMLC
	Organism Scientific	:	STREPTOCOCCUS SUIS
	Organism Taxid	:	1307
	Strain	:	SEROTYPE 2
	Synonym	:	DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE

		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	TDX	4	Ligand/Ion	THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	TDX	2	Ligand/Ion	THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	TDX	2	Ligand/Ion	THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU B:52 , NI B:9603 , HOH B:9620 , HOH B:9632 , GLU C:52 , HOH C:9772 , HOH C:9814	BINDING SITE FOR RESIDUE NI C 9602
2	AC2	SOFTWARE	HOH B:9620 , HOH B:9632 , HOH B:9656 , GLY C:49 , NI C:9602 , HOH C:9642 , HOH C:9772	BINDING SITE FOR RESIDUE NI B 9603
3	AC3	SOFTWARE	ARG A:33 , PHE A:36 , GLU A:38 , HOH A:9064 , GLN B:61 , ARG B:73 , GLU B:78 , ASN B:127 , TYR B:140 , TRP B:146 , HOH B:9623 , HOH B:9624 , HOH B:9628 , HOH B:9636 , HOH B:9769	BINDING SITE FOR RESIDUE TDX B 9001
4	AC4	SOFTWARE	GLN A:61 , ASN A:63 , ARG A:73 , HIS A:76 , GLU A:78 , LYS A:82 , ASN A:127 , TYR A:140 , TRP A:146 , HOH A:9008 , HOH A:9010 , HOH A:9026 , HOH A:9028 , HOH A:9036 , HOH A:9040 , HOH A:9046 , HOH A:9071 , HOH A:9072 , HOH A:9096 , ARG B:33 , PHE B:36 , GLU B:38	BINDING SITE FOR RESIDUE TDX A 9002
5	AC5	SOFTWARE	GLN C:61 , ARG C:73 , HIS C:76 , GLU C:78 , LYS C:82 , ASN C:127 , TYR C:140 , TRP C:146 , HOH C:9620 , HOH C:9626 , HOH C:9647 , HOH C:9650 , HOH C:9657 , HOH C:9676 , HOH C:9682 , HOH C:9687 , HOH C:9752 , HOH C:9777 , HOH C:9782 , ARG D:33 , PHE D:36 , GLU D:38	BINDING SITE FOR RESIDUE TDX C 9003
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:9009 , HOH D:9011 , HOH D:9021 , HOH D:9023 , HOH D:9035 , HOH D:9046 , HOH D:9053 , HOH D:9075 , HOH D:9079 , HOH D:9104 , HOH D:9168	BINDING SITE FOR RESIDUE TDX D 9004

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

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

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

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

(no "Exon" information available for 1NZC)

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 d1nzca_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                 SCOP domains
               CATH domains 1nzcA00 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
                 1nzc 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: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 d1nzcb_ B: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                 SCOP domains
               CATH domains 1nzcB00 B: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.............hhhhh..hhhhhh..hhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzc B   2 TENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain C from PDB  Type:PROTEIN  Length:194
 aligned with Q8GIQ0_STRSU | Q8GIQ0 from UniProtKB/TrEMBL  Length:197

    Alignment length:194
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    
         Q8GIQ0_STRSU     4 NFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
               SCOP domains d1nzcc_ C: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                               SCOP domains
               CATH domains 1nzcC00 C:4-197 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
                 1nzc C   4 NFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193

Chain D from PDB  Type:PROTEIN  Length:194
 aligned with Q8GIQ0_STRSU | Q8GIQ0 from UniProtKB/TrEMBL  Length:197

    Alignment length:194
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    
         Q8GIQ0_STRSU     4 NFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
               SCOP domains d1nzcd_ D: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                               SCOP domains
               CATH domains 1nzcD00 D:4-197 Jelly Rolls                                                                                                                                                                        CATH domains
           Pfam domains (1) ----------dTDP_sugar_isom-1nzcD01 D:14-189                                                                                                                                                -------- Pfam domains (1)
           Pfam domains (2) ----------dTDP_sugar_isom-1nzcD02 D:14-189                                                                                                                                                -------- Pfam domains (2)
           Pfam domains (3) ----------dTDP_sugar_isom-1nzcD03 D:14-189                                                                                                                                                -------- Pfam domains (3)
           Pfam domains (4) ----------dTDP_sugar_isom-1nzcD04 D:14-189                                                                                                                                                -------- Pfam domains (4)
         Sec.struct. author .......eeee.......eeee..eeee..eeeeeeeehhhhh....hhhhhh....eeeeeeee...eeeeee....eeeee.....eeeeeee.........eeeeee...eeeee...eeeeeee...eeeeeeee.......hhhhhee....................hhhhhh..hhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzc D   4 NFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193

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	d1nzca_	A:
1b	d1nzcc_	C:
1c	d1nzcd_	D:
1d	d1nzcb_	B:

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. Strain: serotype 2. (3)

1a	1nzcC00	C:4-197
1b	1nzcD00	D:4-197
1c	1nzcA00	A:2-197
1d	1nzcB00	B:2-197

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: dTDP_sugar_isom (11)

Streptococcus suis (3)

1a	dTDP_sugar_isom-1nzcD01	D:14-189
1b	dTDP_sugar_isom-1nzcD02	D:14-189
1c	dTDP_sugar_isom-1nzcD03	D:14-189
1d	dTDP_sugar_isom-1nzcD04	D:14-189

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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	Q8GIQ0_STRSU \| Q8GIQ0	:	1nxm 1nyw 2ixl

1nxm	APO STRUCTURE OF RMLC FROM STREPTOCCUS SUIS
1nyw	RMLC STRUCTURE FROM STREPTOCOCCUS SUIS 2 IN COMPLEX WITH DTDP-D-GLUCOSE

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