3KO4 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF D-TYR-TRNA(TYR) DEACYLASE FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH ADP

Authors :   Y. Manickam, T. K. Bhatt, A. Sharma

Date :   13 Nov 09 (Deposition) - 01 Dec 09 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)

Keywords :   Dtd, Deacylase, Adp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. K. Bhatt, M. Yogavel, S. Wydau, R. Berwal, A. Sharma
Ligand-Bound Structures Provide Atomic Snapshots For The Catalytic Mechanism Of D-Amino Acid Deacylase
J. Biol. Chem. V. 285 5917 2010
PubMed-ID: 20007323 | Reference-DOI: 10.1074/JBC.M109.038562

Molecule 1 - D-TYROSYL-TRNA(TYR) DEACYLASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DTD
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	3D7

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ADP	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ADP	-1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:71 , TRP A:72 , PHE B:89 , PHE B:103 , HIS B:104 , ALA B:106 , LYS B:107 , PRO B:109 , HOH B:167	BINDING SITE FOR RESIDUE ADP B 165
2	AC2	SOFTWARE	THR C:71 , TRP C:72 , PHE D:89 , LYS D:107 , PRO D:109 , LYS E:96 , ASN F:161	BINDING SITE FOR RESIDUE ADP C 165
3	AC3	SOFTWARE	PHE C:89 , PHE C:103 , ALA C:106 , PRO C:109 , THR D:71 , TRP D:72	BINDING SITE FOR RESIDUE ADP D 165

(no "SS Bond" information available for 3KO4)

Asymmetric Unit

No.	Residues
1	Gly A:149	-	Pro A:150
2	Gly B:149	-	Pro B:150
3	Gly C:149	-	Pro C:150
4	Gly D:149	-	Pro D:150
5	Gly E:149	-	Pro E:150
6	Gly F:149	-	Pro F:150

(no "SAP(SNP)/Variant" information available for 3KO4)

(no "PROSITE Motif" information available for 3KO4)

(no "Exon" information available for 3KO4)

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:151
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
               SCOP domains d3ko4a_ A: autom         ated matches                                                                                                                            SCOP domains
               CATH domains 3ko4A00 A:1-160           [code=3.50.80.10, no name defined]                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.---------..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko4 A   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160
                                          16        26

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
               SCOP domains d3ko4b_ B: autom         ated matches                                                                                                                             SCOP domains
               CATH domains 3ko4B00 B:1-161           [code=3.50.80.10, no name defined]                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.---------..eeeeee..eeeeeee.....hhhhhhhhhhhhhhheeeee..eeeeee......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko4 B   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160 
                                          16        26

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
               SCOP domains d3ko4c_ C: autom        ated matches                                                                                                                             SCOP domains
               CATH domains 3ko4C00 C:1-160          [code=3.50.80.10, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.--------...eeeeee..eeeeeee.....hhhhhhhhhhhhhhh.....-.......hhhhh.eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhh.....eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko4 C   1 MRVVIQRVKGAILSVR--------KELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNN-NKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10     |   -    |   30        40        50        60      | 70        80        90       100       110       120       130       140       150       160
                                          16       25                                        67 |                                                                                           
                                                                                               69

Chain D from PDB  Type:PROTEIN  Length:151
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
               SCOP domains d3ko4d_ D: autom          ated matches                                                                                                                            SCOP domains
               CATH domains 3ko4D00 D:1-161            [code=3.50.80.10, no name defined]                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.----------.eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhh.hhh.eee......eeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko4 D   1 MRVVIQRVKGAILSVR----------LEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10     |   -      | 30        40        50        60        70        80        90       100       110       120       130       140       150       160 
                                          16         27

Chain E from PDB  Type:PROTEIN  Length:150
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
               SCOP domains d3ko4e_ E: autom          ated matches                                                                                                                           SCOP domains
               CATH domains 3ko4E00 E:1-160            [code=3.50.80.10, no name defined]                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.----------.eeeeee..eeeeeee.....hhhhhhhhhhhhhhh.............hhhhh.eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhh...eee......eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko4 E   1 MRVVIQRVKGAILSVR----------LEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10     |   -      | 30        40        50        60        70        80        90       100       110       120       130       140       150       160
                                          16         27

Chain F from PDB  Type:PROTEIN  Length:152
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
               SCOP domains d3ko4f_ F: autom         ated matches                                                                                                                             SCOP domains
               CATH domains 3ko4F00 F:1-161           [code=3.50.80.10, no name defined]                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.---------..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko4 F   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160 
                                          16        26

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 '\|'

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: automated matches (15)

Protein domain: automated matches (15)

Plasmodium falciparum [TaxId: 36329] (13)

1a	d3ko4a_	A:
1b	d3ko4b_	B:
1c	d3ko4c_	C:
1d	d3ko4d_	D:
1e	d3ko4e_	E:
1f	d3ko4f_	F:

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)

Plasmodium falciparum. Organism_taxid: 36329. Strain: 3d7. (10)

1a	3ko4B00	B:1-161
1b	3ko4F00	F:1-161
1c	3ko4A00	A:1-160
1d	3ko4C00	C:1-160
1e	3ko4D00	D:1-161
1f	3ko4E00	E:1-160

(no "Pfam Domain" information available for 3KO4)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q8IIS0_PLAF7 | Q8IIS0)

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.
	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.
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: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:149 - Pro A:150	[ RasMol ]
		Gly B:149 - Pro B:150	[ RasMol ]
		Gly C:149 - Pro C:150	[ RasMol ]
		Gly D:149 - Pro D:150	[ RasMol ]
		Gly E:149 - Pro E:150	[ RasMol ]
		Gly F:149 - Pro F:150	[ RasMol ]

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	3ko4
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Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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