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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT T145A SQD1 PROTEIN COMPLEX WITH NAD AND UDP-SULFOQUINOVOSE/UDP-GLUCOSE
 
Authors :  M. J. Theisen, S. L. Sanda, S. L. Ginell, C. Benning, R. M. Garavito
Date :  07 Feb 01  (Deposition) - 01 Jul 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (4x)
Keywords :  Sdr, Short-Chain Dehydrogenase/Reductase, Rossmann Fold, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Theisen, S. L. Sanda, S. L. Ginell, C. Benning, R. M. Garavito
Characterization Of The Active Site Of Udp-Sulfoquinovose Synthase: Formation Of The Sulfonic Acid Product In The Crystalline State
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSQD1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SQD1
    Mutation: YES
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Strain: COLUMBIA (COL-2)

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO42Ligand/IonSULFATE ION
3UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
4USQ1Ligand/IonSULFOQUINOVOSE-URIDINE-C1,5'-DIPHOSPHATE
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO44Ligand/IonSULFATE ION
3UPG2Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
4USQ2Ligand/IonSULFOQUINOVOSE-URIDINE-C1,5'-DIPHOSPHATE
Biological Unit 2 (4, 20)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO48Ligand/IonSULFATE ION
3UPG4Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
4USQ4Ligand/IonSULFOQUINOVOSE-URIDINE-C1,5'-DIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:294 , GLU A:296 , GLN A:297 , HIS A:339 , HOH A:695 , HOH A:710BINDING SITE FOR RESIDUE SO4 A 403
2AC2SOFTWAREHIS A:20 , LYS A:24 , HOH A:717 , HOH A:945BINDING SITE FOR RESIDUE SO4 A 404
3AC3SOFTWAREGLY 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 , GLU A:99 , ARG A:101 , ASN A:119 , LEU A:143 , TYR A:182 , LYS A:186 , GLN A:209 , GLY A:210 , VAL A:212 , HOH A:440 , HOH A:441 , HOH A:442 , HOH A:443 , HOH A:444 , HOH A:620 , UPG A:1402 , USQ A:2402BINDING SITE FOR RESIDUE NAD A 401
4AC4SOFTWAREARG A:101 , ALA A:103 , ALA 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:420 , HOH A:422 , HOH A:460 , HOH A:463BINDING SITE FOR RESIDUE UPG A 1402
5AC5SOFTWAREARG A:101 , ALA A:103 , ALA 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:420 , HOH A:422 , HOH A:460 , HOH A:463BINDING SITE FOR RESIDUE USQ A 2402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I2B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I2B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I2B)

(-) Exons   (0, 0)

(no "Exon" information available for 1I2B)

(-) 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:393
 aligned with SQD1_ARATH | O48917 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:393
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473   
           SQD1_ARATH    84 PKRVMVIGGDGYCGWATALHLSKKNYEVCIVDNLVRRLFDHQLGLESLTPIASIHDRISRWKALTGKSIELYVGDICDFEFLAESFKSFEPDSVVHFGEQRSAPYSMIDRSRAVYTQHNNVIGTLNVLFAIKEFGEECHLVKLGTMGEYGTPNIDIEEGYITITHNGRTDTLPYPKQASSFYHLSKVHDSHNIAFTCKAWGIRATDLNQGVVYGVKTDETEMHEELRNRLDYDAVFGTALNRFCVQAAVGHPLTVYGKGGQTRGYLDIRDTVQCVEIAIANPAKAGEFRVFNQFTEQFSVNELASLVTKAGSKLGLDVKKMTVPNPRVEAEEHYYNAKHTKLMELGLEPHYLSDSLLDSLLNFAVQFKDRVDTKQIMPSVSWKKIGVKTKSMT 476
               SCOP domains d1i2ba_ A: Sulfolipid biosynthesis protein SQD1                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1i2bA01 A:1-209,A:268-294 NAD(P)-binding Rossmann-like Domain                                                                                                                                                    1i2bA02 A:210-267,A:295-378                               1i2bA01 A:1-209,A:268-294  1i2bA02 A:210-267,A:295-378 UDP-galactose 4-epimerase, domain 1                     --------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 1i2b A   1 GSRVMVIGGDGYCGWATALHLSKKNYEVCIVDNLVRRLFDHQLGLESLTPIASIHDRISRWKALTGKSIELYVGDICDFEFLAESFKSFEPDSVVHFGEQRSAPYSMIDRSRAVYTQHNNVIGTLNVLFAIKEFGEECHLVKLGAMGEYGTPNIDIEEGYITITHNGRTDTLPYPKQASSFYHLSKVHDSHNIAFTCKAWGIRATDLNQGVVYGVKTDETEMHEELRNRLDYDAVFGTALNRFCVQAAVGHPLTVYGKGGQTRGYLDIRDTVQCVEIAIANPAKAGEFRVFNQFTEQFSVNELASLVTKAGSKLGLDVKKMTVPNPRVEAEEHYYNAKHTKLMELGLEPHYLSDSLLDSLLNFAVQFKDRVDTKQIMPSVSWKKIGVKTKSMT 393
                                    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       330       340       350       360       370       380       390
   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)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I2B)

(-) 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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SQD1_ARATH | O48917: 1i24 1i2c 1qrr

(-) Related Entries Specified in the PDB File

1qrr CRYSTAL STRUCTURE OF SQD1 PROTEIN COMPLEX WITH NAD AND UDP- GLUCOSE