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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI YGJD-YEAZ HETERODIMER IN COMPLEX WITH ADP
 
Authors :  W. Zhang, B. Collinet, L. Perrochia, D. Durand, H. Van Tilbeurgh
Date :  23 Feb 15  (Deposition) - 04 Mar 15  (Release) - 04 Mar 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 :  Ygjd-Yeaz Complex, T6A Transferase, 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
    Expression System Taxid: 562
    Gene: TSAD, GCP, YGJD, B3064, JW3036
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: YGJD,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 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Gene: TSAB, YEAZ, B1807, JW1796
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: YEAZ,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  (4, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1ACT13Ligand/IonACETATE ION
2ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
3FE2Ligand/IonFE (III) ION
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3FE-1Ligand/IonFE (III) ION
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3FE-1Ligand/IonFE (III) ION
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:111 , HIS A:115 , SER A:136 , GLY A:137 , GLY A:163 , ASP A:167 , PRO A:181 , GLY A:268 , VAL A:269 , ASN A:272 , THR A:299 , ASP A:300 , FE A:403 , HOH A:522 , HOH A:531 , HOH A:565 , HOH A:569 , HOH A:580 , HOH A:592 , HOH A:604binding site for residue ADP A 401
02AC2SOFTWAREASP A:11 , GLU A:12 , HOH A:580 , HOH A:586 , HOH A:604binding site for residue MG A 402
03AC3SOFTWAREHIS A:111 , HIS A:115 , ASP A:300 , ADP A:401binding site for residue FE A 403
04AC4SOFTWAREMET A:310 , VAL A:311 , LYS A:314binding site for residue ACT A 404
05AC5SOFTWARETHR B:318 , ALA B:319binding site for residue ACT A 405
06AC6SOFTWAREHOH A:514 , ASP B:103binding site for residue ACT A 406
07AC7SOFTWAREPHE A:100 , ALA A:101 , LEU C:53binding site for residue ACT A 407
08AC8SOFTWAREHIS B:111 , HIS B:115 , SER B:136 , GLY B:137 , GLY B:163 , ASP B:167 , GLY B:180 , GLY B:268 , VAL B:269 , ASN B:272 , THR B:299 , ASP B:300 , FE B:403 , HOH B:525 , HOH B:559 , HOH B:566 , HOH B:573 , HOH B:606 , HOH B:607 , HOH B:608binding site for residue ADP B 401
09AC9SOFTWAREASP B:11 , GLU B:12 , HOH B:605 , HOH B:606binding site for residue MG B 402
10AD1SOFTWAREHIS B:111 , HIS B:115 , ASP B:300 , ADP B:401binding site for residue FE B 403
11AD2SOFTWAREPRO B:205 , ARG B:253 , ACT B:405 , HOH B:620binding site for residue ACT B 404
12AD3SOFTWARETHR B:202 , PRO B:205 , ACT B:404binding site for residue ACT B 405
13AD4SOFTWAREVAL A:85 , ARG C:32 , GLU C:33 , HIS C:34 , THR C:35 , SER C:67 , ILE C:73 , ARG C:118 , ACT C:302 , HOH C:422 , HOH C:425 , HOH C:426binding site for residue ADP C 301
14AD5SOFTWAREARG C:32 , ADP C:301binding site for residue ACT C 302
15AD6SOFTWAREALA C:108 , THR C:109 , ARG C:110 , GLU C:159 , VAL C:161binding site for residue ACT C 303
16AD7SOFTWAREVAL B:85 , HOH B:615 , ARG D:32 , GLU D:33 , HIS D:34 , THR D:35 , SER D:67 , THR D:69 , ILE D:73 , ARG D:118 , ACT D:304 , HOH D:433 , HOH D:446 , HOH D:457 , HOH D:466binding site for residue ADP D 301
17AD8SOFTWAREVAL D:143 , LEU D:218 , ASN D:220 , ASN D:221 , HOH D:493binding site for residue ACT D 302
18AD9SOFTWARETHR D:109 , ARG D:110 , GLU D:159 , VAL D:161binding site for residue ACT D 303
19AE1SOFTWAREARG D:32 , ADP D:301binding site for residue ACT D 304
20AE2SOFTWAREGLY D:66 , PHE D:68 , ALA D:117 , TYR D:123 , ARG D:219 , HOH D:457 , HOH D:497binding site for residue ACT D 305
21AE3SOFTWAREVAL B:52 , ARG B:53 , PRO B:57 , HOH B:586 , GLN D:79 , GLU D:211 , ALA D:213 , HOH D:477binding site for residue ACT D 306

(-) 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 4YDU)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YDU)

(-) 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...eeeeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.......eeeeee....eeeeeeee..eeeeeee....hhhhhhhhhhhhh.....hhhhhhhhhh......................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eee..hhhhh...hhhhhhhhhhhhhh..............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ydu A   1 MRVLGIETSCDETGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLVGALLVGATVGRSLAFAWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIKCKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPA 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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               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.....hhhhhhhhhhhh....................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eee..hhhhh...hhhhhhhhhhhhhh..............hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ydu B   1 MRVLGIETSCDETGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLVGALLVGATVGRSLAFAWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIKCKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPAAH 338
                                    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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee.....eehhhhheeehhhhhhhhhhh...eeeee.hhhhhh.........eeee......hhhhhhhhhhhhhhhh...hhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ydu C   1 MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLRNNVAWKKLPGK 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230


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...eeeee.hhhhhh.........eeeeeee...hhhhhhhhhhhhhhh....hhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ydu 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)
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 25)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TSAB_ECOLI | P76256: 1okj 4wq4 4wq5
        TSAD_ECOLI | P05852: 4wq4 4wq5

(-) Related Entries Specified in the PDB File

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