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(-) Description

Title :  STRUCTURE OF A SALMONELLA TYPHIMURIUM YGJD-YEAZ HETERODIMER.
 
Authors :  C. E. Nichols, H. K. Lamb, P. Thompson, K. El Omari, M. Lockyer, I. Charl A. R. Hawkins, D. K. Stammers
Date :  07 Dec 12  (Deposition) - 20 Mar 13  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Yjee, Nucleotide Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. Nichols, H. K. Lamb, P. Thompson, K. E. Omari, M. Lockyer, I. Charles, A. R. Hawkins, D. K. Stammers
Crystal Structure Of The Dimer Of Two Essential Salmonella Typhimurium Proteins, Ygjd & Yeaz And Calorimetric Evidence For The Formation Of A Ternary Ygjd-Yeaz-Yjee Complex.
Protein Sci. V. 22 628 2013
PubMed-ID: 23471679  |  Reference-DOI: 10.1002/PRO.2247

(-) Compounds

Molecule 1 - PUTATIVE M22 PEPTIDASE YEAZ
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. ST4/74
    Organism Taxid: 909946
    Synonym: YEAZ
 
Molecule 2 - PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. ST4/74
    Organism Taxid: 909946
    Other Details: TITLE STRUCTURE OF A SALMONELLA TYPHIMURIUM YGJD-YEAZ HETERODIMER.
    Synonym: YGJD, T(6)A37 THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2CD1Ligand/IonCADMIUM ION
3TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:67 , PHE A:68 , THR A:69 , ARG A:118BINDING SITE FOR RESIDUE TAM A 400
2AC2SOFTWAREHIS B:115 , SER B:136 , GLY B:137 , GLY B:163 , ASP B:167 , GLY B:180 , PRO B:181 , GLY B:267 , GLY B:268 , VAL B:269 , ASN B:272 , ASP B:300 , CD B:401 , HOH B:2092BINDING SITE FOR RESIDUE AMP B 400
3AC3SOFTWAREHIS B:111 , HIS B:115 , ASP B:300 , AMP B:400 , HOH B:2047 , HOH B:2048BINDING SITE FOR RESIDUE CD B 401

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:13 -A:30

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:64 -Pro A:65
2Gly B:81 -Pro B:82
3Phe B:128 -Pro B:129
4Tyr B:177 -Pro B:178

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZET)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZET)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZET)

(-) Sequences/Alignments

Asymmetric/Biological 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:226
 aligned with E8X8J1_SALT4 | E8X8J1 from UniProtKB/TrEMBL  Length:231

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
         E8X8J1_SALT4     1 MRILAIDTATEACSVALWNNGTINAHFELCPREHTQRILPMVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLPMIGVSTLATMAQGAWRKTGATRVLAAIDARMGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLAKECGLTLHDGEVSLPAAEDMLPIASQKLAAGETVAVEHAEPVYLRNEVAWKKLPG 229
               SCOP domains d3zeta1 A:1-107 automated matches                                                                          d3zeta2 A:108-229 automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh..hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..eeeeee......eeeeeeee.....eehhhhheeehhhhhhhhhhhh..eeeee.hhhhhhhhhh---..eeee......hhhhhhhhhhhhhhh....hhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zet A   1 MRILAIDTATEACSVALWNNGTINAHFELCPREHTQRILPMVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLPMIGVSTLATMAQGAWRKTGATRVLAAIDARMGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLA---GLTLHDGEVSLPAAEDMLPIASQKLAAGETVAVEHAEPVYLRNEVAWKKLPG 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   |   180       190       200       210       220         
                                                                                                                                                                                                       174 178                                                   


Chain B from PDB  Type:PROTEIN  Length:337
 aligned with E8XBD7_SALT4 | E8XBD7 from UniProtKB/TrEMBL  Length:337

    Alignment length:337
                                    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       
         E8XBD7_SALT4     1 MRVLGIETSCDETGIAIYDDKKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKEAGLTASDIDAVAYTAGPGLVGALLVGATVGRSLAFAWNVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPMLSKMASQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRSNGGDEQTRADIARAFEDAVVDTLMIKCKRALESTGFKRLVMAGGVSANRTLRAKLAEMMQKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGVTADLGVTVRPRWPLAELPAA 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee...eeeeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.......eeeeee....eeeeeeee..eeeeeee....hhhhhhhhhhhhh.....hhhhhhhhhh......................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eee..hhhhh...hhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zet B   1 MRVLGIETSCDETGIAIYDDKKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKEAGLTASDIDAVAYTAGPGLVGALLVGATVGRSLAFAWNVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPMLSKMASQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRSNGGDEQTRADIARAFEDAVVDTLMIKCKRALESTGFKRLVMAGGVSANRTLRAKLAEMMQKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGVTADLGVTVRPRWPLAELPAA 337
                                    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
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZET)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZET)

(-) Gene Ontology  (12, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (E8X8J1_SALT4 | E8X8J1)
biological process
    GO:0002949    tRNA threonylcarbamoyladenosine modification    The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base).

Chain B   (E8XBD7_SALT4 | E8XBD7)
molecular function
    GO:0061711    N(6)-L-threonylcarbamoyladenine synthase    Catalysis of the reaction: L-threonylcarbamoyladenylate + adenine(37) in tRNA = AMP + N(6)-L-threonylcarbamoyladenine(37) in tRNA.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0002949    tRNA threonylcarbamoyladenosine modification    The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3zeu STRUCTURE OF A SALMONELLA TYPHIMURIUM YGJD-YEAZ HETERODIMER BOUND TO ATPGAMMAS