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(-) Description

Title :  STRUCTURE OF YIHT FROM SALMONELLA TYPHIMURIUM
 
Authors :  J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  11 Jun 04  (Deposition) - 22 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Beta-Alpha Barrel, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Gorman, L. Shapiro
Structure Of Yiht From Salmonella Typhimurium
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE ALDOLASE YIHT
    Chains: A
    EC Number: 4.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YIHT, STM4022
    Mutation: YES
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric Unit (3, 23)
No.NameCountTypeFull Name
1BR9Ligand/IonBROMIDE ION
2MSE11Mod. Amino AcidSELENOMETHIONINE
3PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 28)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MSE22Mod. Amino AcidSELENOMETHIONINE
3PO46Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:182 , ARG A:213 , HIS A:217BINDING SITE FOR RESIDUE PO4 A 303
02AC2SOFTWAREGLN A:23 , GLU A:159 , LYS A:193 , ARG A:253 , PO4 A:305 , HOH A:372 , HOH A:378 , HOH A:394BINDING SITE FOR RESIDUE PO4 A 304
03AC3SOFTWARELYS A:193 , SER A:226 , SER A:227 , ALA A:251 , GLY A:252 , ARG A:253 , PO4 A:304BINDING SITE FOR RESIDUE PO4 A 305
04AC4SOFTWAREGLY A:202BINDING SITE FOR RESIDUE BR A 306
05AC5SOFTWAREPRO A:100 , VAL A:101 , ARG A:163BINDING SITE FOR RESIDUE BR A 307
06AC6SOFTWAREVAL A:40BINDING SITE FOR RESIDUE BR A 308
07AC7SOFTWAREASP A:172 , HOH A:357 , HOH A:384BINDING SITE FOR RESIDUE BR A 309
08AC8SOFTWAREARG A:204 , ARG A:239BINDING SITE FOR RESIDUE BR A 310
09AC9SOFTWAREASP A:47 , PHE A:48 , ASN A:51 , HOH A:386BINDING SITE FOR RESIDUE BR A 311
10BC1SOFTWAREASP A:264 , LEU A:267BINDING SITE FOR RESIDUE BR A 312
11BC2SOFTWAREARG A:11 , SER A:61 , BR A:314BINDING SITE FOR RESIDUE BR A 313
12BC3SOFTWAREARG A:11 , ALA A:12 , BR A:313BINDING SITE FOR RESIDUE BR A 314

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TO3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:38 -Pro A:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TO3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TO3)

(-) Exons   (0, 0)

(no "Exon" information available for 1TO3)

(-) 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:291
 aligned with SQUT_SALTY | Q9L7R9 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:291
                                    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 
           SQUT_SALTY     1 MNNYTIKDITRASGGFAMLAVDQREAMRLMFAAAGAKTPVADSVLTDFKVNAAKILSPYASAVLLDQQFCYRQAVEQNAVAKSCAMIVAADDFIPGNGIPVDNVVLDKKINAQAVKRDGAKALKLLVLWRSDEDAQQRLNMVKEFNELCHSNGLLSIIEPVVRPPRCGDKFDREQAIIDAAKELGDSGADLYKVEMPLYGKGARSDLLTASQRLNGHINMPWVILSSGVDEKLFPRAVRVAMEAGASGFLAGRAVWSSVIGLPDTELMLRDVSAPKLQRLGEIVDEMMAKR 291
               SCOP domains d1to3a_ A: Putative aldolase YihT                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1to3A00 A:1-291 Aldolase class I                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.....eeeee...hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhh.......eeeee.eeeeee..eeeeeeee....hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhh.....eeee.hhhhhh.hhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh...eeeehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to3 A   1 LNNYTIKDITRASGGFAmLAVDQREAmRLmFAAAGAKTPVADSVLTDFKVNAAKILSPYASAVLLDQQFCYRQAVEQNAVAKSCAmIVAADDFIPGNGIPVDNVVLDKKINAQAVKRDGAKALKLLVLWRSDEDAQQRLNmVKEFNELCHSNGLLSIIEPVVRPPRCGDKFDREQAIIDAAKELGDSGADLYKVEmPLYGKGARSDLLTASQRLNGHINmPWVILSSGVDEKLFPRAVRVAmEAGASGFLAGRAVWSSVIGLPDTELmLRDVSAPKLQRLGEIVDEmmGKR 291
                                    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 
                                            18-MSE   27-MSE                                                     86-MSE                                                141-MSE                                                196-MSE                 220-MSE               242-MSE                   268-MSE            287-MSE
                                                        30-MSE                                                                                                                                                                                                                                                           288-MSE
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TO3)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (SQUT_SALTY | Q9L7R9)
molecular function
    GO:0061595    6-deoxy-6-sulfofructose-1-phosphate aldolase activity    Catalysis of the reaction 6-deoxy-6-sulfofructose-1-phosphate = 3-sulfolactaldehyde + dihydroxyacetone phosphate.
    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: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.
biological process
    GO:1902777    6-sulfoquinovose(1-) catabolic process    The chemical reactions and pathways resulting in the breakdown of 6-sulfoquinovose(1-).

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