1R6D - JenaLib

Title :   CRYSTAL STRUCTURE OF DESIV DOUBLE MUTANT (DTDP-GLUCOSE 4,6-DEHYDRATASE) FROM STREPTOMYCES VENEZUELAE WITH NAD AND DAU BOUND

Authors :   S. T. M. Allard, W. W. Cleland, H. M. Holden

Date :   14 Oct 03 (Deposition) - 27 Jan 04 (Release) - 23 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Dehydratase, Rossmann Fold, Short-Chain Dehydrogenase/Reductase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. T. M. Allard, W. W. Cleland, H. M. Holden
High Resolution X-Ray Structure Of Dtdp-Glucose 4, 6-Dehydratase From Streptomyces Venezuelae
J. Biol. Chem. V. 279 2211 2004
PubMed-ID: 14570895 | Reference-DOI: 10.1074/JBC.M310134200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:7 , ALA A:9 , GLY A:10 , PHE A:11 , ILE A:12 , ASP A:37 , SER A:38 , LEU A:39 , THR A:40 , ALA A:42 , GLY A:43 , GLY A:62 , ASP A:63 , ILE A:64 , PHE A:83 , ALA A:84 , ALA A:85 , SER A:87 , THR A:102 , VAL A:125 , SER A:126 , TYR A:151 , LYS A:155 , CYS A:178 , CYS A:179 , ASN A:180 , ASN A:181 , DAU A:401 , HOH A:504 , HOH A:512 , HOH A:514 , HOH A:516 , HOH A:520 , HOH A:526 , HOH A:538 , HOH A:560 , HOH A:655	BINDING SITE FOR RESIDUE NAD A 400
2	AC2	SOFTWARE	SER A:87 , HIS A:88 , VAL A:89 , THR A:127 , ASN A:128 , GLN A:129 , TYR A:151 , ASN A:180 , GLU A:189 , LYS A:190 , LEU A:191 , LEU A:194 , PRO A:206 , LEU A:207 , TYR A:208 , ARG A:215 , ASN A:250 , ARG A:274 , HIS A:277 , TYR A:281 , NAD A:400 , HOH A:502 , HOH A:552 , HOH A:559 , HOH A:804	BINDING SITE FOR RESIDUE DAU A 401

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:322
 aligned with Q9ZGH3_STRVZ | Q9ZGH3 from UniProtKB/TrEMBL  Length:337

    Alignment length:322
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  
         Q9ZGH3_STRVZ     1 MRLLVTGGAGFIGSHFVRQLLAGAYPDVPADEVIVLDSLTYAGNRANLAPVDADPRLRFVHGDIRDAGLLARELRGVDAIVHFAAESHVDRSIAGASVFTETNVQGTQTLLQCAVDAGVGRVVHVSTDEVYGSIDSGSWTESSPLEPNSPYAASKAGSDLVARAYHRTYGLDVRITRCCNNYGPYQHPEKLIPLFVTNLLDGGTLPLYGDGANVREWVHTDDHCRGIALVLAGGRAGEIYHIGGGLELTNRELTGILLDSLGADWSSVRKVADRKGHDLRYSLDGGEIERELGYRPQVSFADGLARTVRWYRENRGWWEPLK 322
               SCOP domains d1r6da_ A: dTDP-glucose 4,6-dehydratase (RmlB)                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1r6dA01 A:1-179,A:220-242,A:282-297 NAD(P)-binding Rossmann-like Domain                                                                                                            1r6dA02 A:180-219,A:243-273,A:298-322   1r6dA01                1r6dA02                        --------1r6dA01         1r6dA02                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh........eeeeee......hhhhhhhhh....eeeee....hhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee.......hhhhhhhhhhhh...eeee.....eeeeeehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhh..hhh.eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r6d A   1 MRLLVTGGAGFIGSHFVRQLLAGAYPDVPADEVIVLDSLTYAGNRANLAPVDADPRLRFVHGDIRDAGLLARELRGVDAIVHFAAESHVDRSIAGASVFTETNVQGTQTLLQCAVDAGVGRVVHVSTNQVYGSIDSGSWTESSPLEPNSPYAASKAGSDLVARAYHRTYGLDVRITRCCNNYGPYQHPEKLIPLFVTNLLDGGTLPLYGDGANVREWVHTDDHCRGIALVLAGGRAGEIYHIGGGLELTNRELTGILLDSLGADWSSVRKVADRKGHDLRYSLDGGKIERELGYRPQVSFADGLARTVRWYRENRGWWEPLK 322
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

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, 1)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A (Q9ZGH3_STRVZ | Q9ZGH3)

molecular function
	GO:0008460	dTDP-glucose 4,6-dehydratase activity	Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(2)O.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0009225	nucleotide-sugar metabolic process	The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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