1JKE - JenaLib

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Biological Unit 6 (Jmol Viewer)

Biological Unit 7 (Jmol Viewer)

Title :   D-TYR TRNATYR DEACYLASE FROM ESCHERICHIA COLI

Authors :   M. L. Ferri-Fioni, E. Schmitt, J. Soutourina, P. Plateau, Y. Mechulam, S. Blanquet

Date :   12 Jul 01 (Deposition) - 25 Jan 02 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,C  (1x)
Biol. Unit 3: A (2x),B (2x),C (2x),D (2x)
Biol. Unit 4: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 5: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 6: A,C  (1x)
Biol. Unit 7: B (1x),D (1x)

Keywords :   Beta-Alpha-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. L. Ferri-Fioni, E. Schmitt, J. Soutourina, P. Plateau, Y. Mechulam S. Blanquet
Structure Of Crystalline D-Tyr-Trna(Tyr) Deacylase. A Representative Of A New Class Of Trna-Dependent Hydrolases.
J. Biol. Chem. V. 276 47285 2001
PubMed-ID: 11568181 | Reference-DOI: 10.1074/JBC.M106550200

Molecule 1 - D-TYR-TRNATYR DEACYLASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK223-3
	Expression System Strain	:	JM101TR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YIHZ OR B3887
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	O145

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C
Biological Unit 3 (2x)	:	A (2x)	B (2x)	C (2x)	D (2x)
Biological Unit 4 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)
Biological Unit 5 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)
Biological Unit 6 (1x)	:	A		C
Biological Unit 7 (1x)	:		B (1x)		D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	ZN	12	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 7 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP B:107 , GLU B:111 , ASP C:100 , GLU D:18	BINDING SITE FOR RESIDUE ZN D 901
02	AC2	SOFTWARE	GLU B:18 , GLU D:103 , ASP D:107 , HOH D:1087 , HOH D:1088	BINDING SITE FOR RESIDUE ZN D 902
03	AC3	SOFTWARE	GLU B:22 , HOH B:1020 , HOH B:1021 , GLU D:111 , HOH D:1270	BINDING SITE FOR RESIDUE ZN D 903
04	AC4	SOFTWARE	ASP D:100 , HOH D:1103 , HOH D:1376	BINDING SITE FOR RESIDUE ZN D 904
05	AC5	SOFTWARE	GLU A:18 , HOH A:1134 , GLU C:103 , ASP C:107	BINDING SITE FOR RESIDUE ZN C 905
06	AC6	SOFTWARE	GLU A:16 , HOH A:1325 , GLU B:47	BINDING SITE FOR RESIDUE ZN A 906
07	AC7	SOFTWARE	ASP B:128 , ASP D:36 , HOH D:1184 , HOH D:1189	BINDING SITE FOR RESIDUE ZN D 907
08	AC8	SOFTWARE	GLU A:111 , HOH A:1234 , GLU C:22 , HOH C:1230 , HOH C:1350 , HOH C:1353	BINDING SITE FOR RESIDUE ZN A 908
09	AC9	SOFTWARE	GLU A:103 , ASP A:107 , GLU C:18 , HOH C:1404 , HOH C:1416	BINDING SITE FOR RESIDUE ZN A 909
10	BC1	SOFTWARE	GLU C:117 , HOH C:1308 , HOH C:1316 , HOH C:1414 , HOH C:1415	BINDING SITE FOR RESIDUE ZN C 910
11	BC2	SOFTWARE	LYS C:41 , HOH C:1044 , HOH C:1105 , HOH C:1118 , HOH C:1288 , HOH C:1378 , HOH C:1380	BINDING SITE FOR RESIDUE ZN C 911
12	BC3	SOFTWARE	HOH B:1254 , HOH B:1370 , HOH B:1413 , HOH B:1417 , HOH B:1418 , HOH B:1419	BINDING SITE FOR RESIDUE ZN B 912

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

Asymmetric Unit

No.	Residues
1	Gly A:137	-	Pro A:138
2	Gly B:137	-	Pro B:138
3	Gly C:137	-	Pro C:138
4	Gly D:137	-	Pro D:138

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

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

(no "Exon" information available for 1JKE)

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:145
 aligned with DTD_ECOLI | P0A6M4 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            DTD_ECOLI     1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV 145
               SCOP domains d1jkea_ A: D-Tyr tRNAtyr deacylase, DTD                                                                                                           SCOP domains
               CATH domains 1jkeA00 A:1-145  [code=3.50.80.10, no name defined]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhh............eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jke A   1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV 145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:145
 aligned with DTD_ECOLI | P0A6M4 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            DTD_ECOLI     1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV 145
               SCOP domains d1jkeb_ B: D-Tyr tRNAtyr deacylase, DTD                                                                                                           SCOP domains
               CATH domains 1jkeB00 B:1-145  [code=3.50.80.10, no name defined]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh...........eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jke B   1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV 145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:145
 aligned with DTD_ECOLI | P0A6M4 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            DTD_ECOLI     1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV 145
               SCOP domains d1jkec_ C: D-Tyr tRNAtyr deacylase, DTD                                                                                                           SCOP domains
               CATH domains 1jkeC00 C:1-145  [code=3.50.80.10, no name defined]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh..eee......eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jke C   1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV 145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:145
 aligned with DTD_ECOLI | P0A6M4 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            DTD_ECOLI     1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV 145
               SCOP domains d1jked_ D: D-Tyr tRNAtyr deacylase, DTD                                                                                                           SCOP domains
               CATH domains 1jkeD00 D:1-145  [code=3.50.80.10, no name defined]                                                                                               CATH domains
           Pfam domains (1) -Tyr_Deacylase-1jkeD01 D:2-145                                                                                                                    Pfam domains (1)
           Pfam domains (2) -Tyr_Deacylase-1jkeD02 D:2-145                                                                                                                    Pfam domains (2)
           Pfam domains (3) -Tyr_Deacylase-1jkeD03 D:2-145                                                                                                                    Pfam domains (3)
           Pfam domains (4) -Tyr_Deacylase-1jkeD04 D:2-145                                                                                                                    Pfam domains (4)
         Sec.struct. author .eeeeeeeeeeeeee..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhh...eee......eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jke D   1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV 145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: DTD-like (18)

Superfamily: DTD-like (18)

Family: DTD-like (3)

Protein domain: D-Tyr tRNAtyr deacylase, DTD (2)

Escherichia coli [TaxId: 562] (1)

1a	d1jkea_	A:
1b	d1jkeb_	B:
1c	d1jkec_	C:
1d	d1jked_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: D-tyrosyl-trna(Tyr) Deacylase; Chain: A; (15)

Homologous Superfamily: [code=3.50.80.10, no name defined] (15)

Escherichia coli. Organism_taxid: 562. (1)

1a	1jkeA00	A:1-145
1b	1jkeB00	B:1-145
1c	1jkeC00	C:1-145
1d	1jkeD00	D:1-145

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Tyr_Deacylase] (12)

Family: Tyr_Deacylase (12)

Escherichia coli (strain K12) (1)

1a	Tyr_Deacylase-1jkeD01	D:2-145
1b	Tyr_Deacylase-1jkeD02	D:2-145
1c	Tyr_Deacylase-1jkeD03	D:2-145
1d	Tyr_Deacylase-1jkeD04	D:2-145

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DTD_ECOLI | P0A6M4)

molecular function
	GO:0051500	D-tyrosyl-tRNA(Tyr) deacylase activity	Catalysis of the reaction: D-tyrosyl-tRNA(Tyr) = D-tyrosine + tRNA(Tyr). Hydrolysis of the removal of D-tyrosine from tyrosine residues in charged tRNA.
	GO:0002161	aminoacyl-tRNA editing activity	The hydrolysis of an incorrectly aminoacylated tRNA.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
biological process
	GO:0019478	D-amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.
	GO:0006450	regulation of translational fidelity	Any process that modulates the ability of the translational apparatus to interpret the genetic code.
	GO:0009408	response to heat	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0006399	tRNA metabolic process	The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:137 - Pro A:138	[ RasMol ]
		Gly B:137 - Pro B:138	[ RasMol ]
		Gly C:137 - Pro C:138	[ RasMol ]
		Gly D:137 - Pro D:138	[ RasMol ]

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	1jke
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