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(-) Description

Title :  E. COLI YGJD(E12A)-YEAZ HETERODIMER IN COMPLEX WITH ATP
 
Authors :  W. Zhang, B. Collinet
Date :  21 Oct 14  (Deposition) - 28 Jan 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Heterodimer, Ygjd-Yeaz, Glu12Ala, T6A, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Zhang, B. Collinet, L. Perrochia, D. Durand, H. Van Tilbeurgh
The Atp-Mediated Formation Of The Ygjd-Yeaz-Yjee Complex Is Required For The Biosynthesis Of Trna T6A In Escherichia Coli.
Nucleic Acids Res. V. 43 1804 2015
PubMed-ID: 25578970  |  Reference-DOI: 10.1093/NAR/GKU1397

(-) Compounds

Molecule 1 - TRNA N6-ADENOSINE THREONYLCARBAMOYLTRANSFERASE
    Chains: A, B
    EC Number: 2.6.99.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Plasmid: PET21A-YGJD-E12A
    Expression System Taxid: 866768
    Expression System Vector: PET21A
    Expression System Vector Type: PLASMID
    Gene: TSAD, GCP, YGJD, B3064, JW3036
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: N6-L-THREONYLCARBAMOYLADENINE SYNTHASE,T(6)A SYNTHASE,T(6) A37 THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAD,TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAD
 
Molecule 2 - TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TSAB, YEAZ, B1807, JW1796
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: T(6)A37 THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3FE2Ligand/IonFE (III) ION
4GOL1Ligand/IonGLYCEROL
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3FE-1Ligand/IonFE (III) ION
4GOL1Ligand/IonGLYCEROL
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3FE-1Ligand/IonFE (III) ION
4GOL-1Ligand/IonGLYCEROL
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:111 , HIS A:115 , ASP A:300 , ATP A:402binding site for residue FE A 401
2AC2SOFTWAREHIS A:111 , MET A:112 , HIS A:115 , SER A:136 , GLY A:137 , GLY A:138 , HIS A:139 , GLY A:163 , ASP A:167 , GLY A:180 , PRO A:181 , GLY A:268 , VAL A:269 , ASN A:272 , ASP A:300 , FE A:401 , HOH A:536 , HOH A:538 , HOH A:572 , HOH A:591binding site for residue ATP A 402
3AC3SOFTWAREVAL A:85binding site for residue ACT A 403
4AC4SOFTWAREHIS B:111 , HIS B:115 , ASP B:300 , ATP B:402 , HOH B:527binding site for residue FE B 401
5AC5SOFTWAREMET B:112 , HIS B:115 , SER B:136 , GLY B:137 , GLY B:138 , HIS B:139 , GLY B:163 , PHE B:166 , ASP B:167 , GLY B:180 , PRO B:181 , GLY B:268 , VAL B:269 , ASN B:272 , ASP B:300 , FE B:401 , HOH B:527binding site for residue ATP B 402
6AC6SOFTWAREARG B:49 , ASP B:50 , ARG B:53binding site for residue ACT B 403
7AC7SOFTWAREARG C:32 , GLU C:33 , HIS C:34 , SER C:67 , THR C:69 , ILE C:73 , PEG C:302 , HOH C:425 , HOH C:440binding site for residue GOL C 301
8AC8SOFTWARESER C:67 , PHE C:68 , GOL C:301 , HOH C:463binding site for residue PEG C 302
9AC9SOFTWAREARG D:32 , GLU D:33 , HIS D:34 , THR D:35binding site for residue PEG D 301

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1C:13 -C:30
2D:13 -D:30

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:81 -Pro A:82
2Phe A:128 -Pro A:129
3Tyr A:177 -Pro A:178
4Gly B:81 -Pro B:82
5Phe B:128 -Pro B:129
6Tyr B:177 -Pro B:178
7Gly C:64 -Pro C:65
8Gly D:64 -Pro D:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WQ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WQ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4WQ4)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee...eeeeeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.......eeeeee....eeeeee.....eeeeee....hhhhhhhhhhhhh.....hhhhhhhhhh......................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eee..hhhhhh..hhhhhhhhhhhhhh..............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wq4 A   1 MRVLGIETSCDATGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLVGALLVGATVGRSLAFAWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIKCKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPA 336
                                    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      


Chain B from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee...eeeeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.......eeeeee....eeeeee.....eeeeee....hhhhhhhhhhhhh.....hhhhhhhhhh......................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eee..hhhhh...hhhhhhhhhhhhhh..............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wq4 B   1 MRVLGIETSCDATGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLVGALLVGATVGRSLAFAWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIKCKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPA 336
                                    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      


Chain C from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh..hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee.....eehhhhheeehhhhhhhhhh....eeeeehhhhhhh.........eeee......hhhhhhhhhhhhhhh....hhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wq4 C   1 MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLRNNVAWKKLPG 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         


Chain D from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh..hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee.....eehhhhheeehhhhhhhhhhh...eeeeehhhhhhh.........eeee......hhhhhhhhhhhhhhh....hhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wq4 D   1 MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLRNNVAWKKLPG 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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  (0, 0)

(no "SCOP Domain" information available for 4WQ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WQ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WQ4)

(-) Gene Ontology  (17, 25)

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  4wq4
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  TSAB_ECOLI | P76256
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  TSAD_ECOLI | P05852
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 Related Entries

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

UniProtKB/Swiss-Prot
        TSAB_ECOLI | P76256: 1okj 4wq5 4ydu
        TSAD_ECOLI | P05852: 4wq5 4ydu

(-) Related Entries Specified in the PDB File

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