4WQ5 - JenaLib

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Title :   YGJD(V85E)-YEAZ HETERODIMER IN COMPLEX WITH ATP

Authors :   W. Zhang

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,D  (1x)
Biol. Unit 2: B,C  (1x)

Keywords :   Heterodimer, Ygjd-Yeaz, Val85Glu, 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

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 Taxid	:	866768
	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 'BL21-GOLD(DE3)PLYSS AG'
	Expression System Taxid	:	866768
	Gene	:	TSAB, YEAZ, B1807, JW1796
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	T(6)A37 THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	ACT	8	Ligand/Ion	ACETATE ION
2	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	FE	2	Ligand/Ion	FE (III) ION
4	GOL	1	Ligand/Ion	GLYCEROL
5	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	ACT	6	Ligand/Ion	ACETATE ION
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	FE	-1	Ligand/Ion	FE (III) ION
4	GOL	-1	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	FE	-1	Ligand/Ion	FE (III) ION
4	GOL	1	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:11 , GLU A:12 , ASP A:300 , ATP A:403	binding site for residue MG A 401
02	AC2	SOFTWARE	HIS A:111 , HIS A:115 , ASP A:300 , ATP A:403	binding site for residue FE A 402
03	AC3	SOFTWARE	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 , CYS A:298 , THR A:299 , ASP A:300 , MG A:401 , FE A:402	binding site for residue ATP A 403
04	AC4	SOFTWARE	GLY A:149	binding site for residue ACT A 405
05	AC5	SOFTWARE	ARG A:96 , ALA A:99 , PHE A:100 , VAL A:104	binding site for residue ACT A 406
06	AC6	SOFTWARE	PHE B:100 , ALA B:101 , SER C:52 , LEU C:53	binding site for residue ACT A 407
07	AC7	SOFTWARE	ASP B:11 , GLU B:12 , ASP B:300 , ATP B:403 , HOH B:515	binding site for residue MG B 401
08	AC8	SOFTWARE	HIS B:111 , HIS B:115 , ASP B:300 , ATP B:403	binding site for residue FE B 402
09	AC9	SOFTWARE	MET B:112 , HIS B:115 , SER B:136 , GLY B:137 , GLY B:138 , HIS B:139 , GLY B:163 , ASP B:167 , GLY B:180 , PRO B:181 , GLY B:268 , VAL B:269 , ASN B:272 , CYS B:298 , THR B:299 , ASP B:300 , MG B:401 , FE B:402 , HOH B:515	binding site for residue ATP B 403
10	AD1	SOFTWARE	TYR B:30 , ARG B:53 , LYS B:54	binding site for residue ACT B 404
11	AD2	SOFTWARE	ARG C:32 , GLU C:33 , HIS C:34 , THR C:35	binding site for residue ACT C 301
12	AD3	SOFTWARE	SER C:67 , PHE C:68 , THR C:69 , ARG C:118	binding site for residue GOL C 302
13	AD4	SOFTWARE	ARG D:32 , GLU D:33 , HIS D:34 , THR D:35	binding site for residue ACT D 301
14	AD5	SOFTWARE	SER D:67	binding site for residue ACT D 302

Asymmetric Unit

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

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 4WQ5)

(no "PROSITE Motif" information available for 4WQ5)

(no "Exon" information available for 4WQ5)

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:332
                                                                                                                                                                                                                                                                                                                                                                            
               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..hhhhhh..hhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wq5 A   1 MRVLGIETSCDETGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLEGALLVGATVGRSLAFAWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIKCKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGATADLGVSVRPRWPLA 332
                                    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..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.......eeeeee....eeeeeeee..eeeeeee....hhhhhhhhhhhhh.....hhhhhhhhhhh.....................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eee..hhhhh...hhhhhhhhhhhhhh..............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wq5 B   1 MRVLGIETSCDETGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLEGALLVGATVGRSLAFAWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIKCKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPA 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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee...eeeeeee...hhhhhhhhhhhhhhhhh..hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee.....eehhhhheeehhhhhhhhhh....eeeeehhhhhhh.........eeee......hhhhhhhhhhhhhhh....hhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wq5 C   1 MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLRNNVWKKLP 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 ||    
                                                                                                                                                                                                                                                       222|    
                                                                                                                                                                                                                                                        224

Chain D from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               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....eeeee.hhhhhh.........eeee......hhhhhhhhhhhhhhh....hhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wq5 D   1 MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLRNNVAWKKLP 228
                                    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 '\|'

(no "SCOP Domain" information available for 4WQ5)

(no "CATH Domain" information available for 4WQ5)

(no "Pfam Domain" information available for 4WQ5)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:81 - Pro A:82	[ RasMol ]
		Gly B:81 - Pro B:82	[ RasMol ]
		Gly C:64 - Pro C:65	[ RasMol ]
		Gly D:64 - Pro D:65	[ RasMol ]
		Phe A:128 - Pro A:129	[ RasMol ]
		Phe B:128 - Pro B:129	[ RasMol ]
		Tyr A:177 - Pro A:178	[ RasMol ]
		Tyr B:177 - Pro B:178	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4wq5
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	TSAB_ECOLI \| P76256
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	TSAD_ECOLI \| P05852
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	2.6.99.4
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	TSAB_ECOLI \| P76256
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	TSAD_ECOLI \| P05852
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UniProtKB/Swiss-Prot
	TSAB_ECOLI \| P76256	:	1okj 4wq4 4ydu
	TSAD_ECOLI \| P05852	:	4wq4 4ydu

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (14, 14)

SS Bonds (2, 2)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (17, 25)

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Related Entries

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Related Entries Specified in the PDB File