1QRR - JenaLib

Title :   CRYSTAL STRUCTURE OF SQD1 PROTEIN COMPLEX WITH NAD AND UDP-GLUCOSE

Authors :   A. M. Mulichak, M. J. Theisen, B. Essigmann, C. Benning, R. M. Garavito

Date :   15 Jun 99 (Deposition) - 10 Nov 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Rossmann Fold, Short Hydrogen Bonds, Sdr Homolog, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Mulichak, M. J. Theisen, B. Essigmann, C. Benning, R. M. Garavito
Crystal Structure Of Sqd1, An Enzyme Involved In The Biosynthesis Of The Plant Sulfolipid Headgroup Donor Udp-Sulfoquinovose.
Proc. Natl. Acad. Sci. Usa V. 96 13097 1999
PubMed-ID: 10557279 | Reference-DOI: 10.1073/PNAS.96.23.13097
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:294 , GLU A:296 , GLN A:297 , HIS A:339 , HOH A:695 , HOH A:710	BINDING SITE FOR RESIDUE SO4 A 403
2	AC2	SOFTWARE	HIS A:20 , LYS A:24 , HOH A:717	BINDING SITE FOR RESIDUE SO4 A 404
3	AC3	SOFTWARE	GLY A:8 , GLY A:11 , TYR A:12 , CYS A:13 , ASP A:32 , ASN A:33 , LEU A:34 , VAL A:35 , ARG A:36 , GLY A:74 , ASP A:75 , ILE A:76 , PHE A:97 , GLY A:98 , ARG A:101 , ASN A:119 , LEU A:143 , TYR A:182 , LYS A:186 , GLN A:209 , GLY A:210 , VAL A:212 , UPG A:402 , HOH A:440 , HOH A:441 , HOH A:442 , HOH A:443 , HOH A:444 , HOH A:620	BINDING SITE FOR RESIDUE NAD A 401
4	AC4	SOFTWARE	ARG A:101 , ALA A:103 , THR A:145 , MET A:146 , GLY A:147 , TYR A:182 , HIS A:183 , GLN A:209 , VAL A:211 , THR A:238 , ALA A:239 , ARG A:242 , THR A:254 , TYR A:256 , GLN A:261 , ARG A:263 , VAL A:300 , ARG A:327 , GLU A:329 , NAD A:401 , HOH A:411 , HOH A:420 , HOH A:422 , HOH A:460 , HOH A:461 , HOH A:463	BINDING SITE FOR RESIDUE UPG A 402

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:390
 aligned with SQD1_ARATH | O48917 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:390
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474
           SQD1_ARATH    85 KRVMVIGGDGYCGWATALHLSKKNYEVCIVDNLVRRLFDHQLGLESLTPIASIHDRISRWKALTGKSIELYVGDICDFEFLAESFKSFEPDSVVHFGEQRSAPYSMIDRSRAVYTQHNNVIGTLNVLFAIKEFGEECHLVKLGTMGEYGTPNIDIEEGYITITHNGRTDTLPYPKQASSFYHLSKVHDSHNIAFTCKAWGIRATDLNQGVVYGVKTDETEMHEELRNRLDYDAVFGTALNRFCVQAAVGHPLTVYGKGGQTRGYLDIRDTVQCVEIAIANPAKAGEFRVFNQFTEQFSVNELASLVTKAGSKLGLDVKKMTVPNPRVEAEEHYYNAKHTKLMELGLEPHYLSDSLLDSLLNFAVQFKDRVDTKQIMPSVSWKKIGVKTKS 474
               SCOP domains d1qrra_ A: Sulfolipid biosynthesis protein SQD1                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1qrrA01 A:2-209,A:268-294 NAD(P)-binding Rossmann-like Domain                                                                                                                                                   1qrrA02 A:210-267,A:295-378                               1qrrA01 A:2-209,A:268-294  1qrrA02 A:210-267,A:295-378 UDP-galactose 4-epimerase, domain 1                     ------------- CATH domains
               Pfam domains --Epimerase-1qrrA01 A:4-292                                                                                                                                                                                                                                                                        --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh.........eeeeee..eeeeee......hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee.....hhhhhhhhh..........hhhhhhhhhhhhh..eeee.....eeeeeehhhhhhhhhhhhhh......eeeeee..eeeehhhhhhhhhhhhhh......eeee................hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qrr A   2 KRVMVIGGDGYCGWATALHLSKKNYEVCIVDNLVRRLFDHQLGLESLTPIASIHDRISRWKALTGKSIELYVGDICDFEFLAESFKSFEPDSVVHFGEQRSAPYSMIDRSRAVYTQHNNVIGTLNVLFAIKEFGEECHLVKLGTMGEYGTPNIDIEEGYITITHNGRTDTLPYPKQASSFYHLSKVHDSHNIAFTCKAWGIRATDLNQGVVYGVKTDETEMHEELRNRLDYDAVFGTALNRFCVQAAVGHPLTVYGKGGQTRGYLDIRDTVQCVEIAIANPAKAGEFRVFNQFTEQFSVNELASLVTKAGSKLGLDVKKMTVPNPRVEAEEHYYNAKHTKLMELGLEPHYLSDSLLDSLLNFAVQFKDRVDTKQIMPSVSWKKIGVKTKS 391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391

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 (1, 1)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (SQD1_ARATH | O48917)

molecular function
	GO:0046507	UDPsulfoquinovose synthase activity	Catalysis of the reaction: sulfite + UDP-D-glucose = H(2)O + UDP-6-sulfoquinovose.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0050662	coenzyme binding	Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008146	sulfotransferase activity	Catalysis of the transfer of a sulfate group from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyl group of an acceptor, producing the sulfated derivative and 3'-phosphoadenosine 5'-phosphate.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0016036	cellular response to phosphate starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
	GO:0009247	glycolipid biosynthetic process	The chemical reactions and pathways resulting in the formation of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide).
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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