3KO9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   DTD FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH D-ARGININE

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 :   2.75

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, D-Arginine, 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, 1)

No.	Name	Count	Type	Full Name
1	DAR	1	Ligand/Ion	D-ARGININE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DAR	1	Ligand/Ion	D-ARGININE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	DAR	-1	Ligand/Ion	D-ARGININE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	DAR	-1	Ligand/Ion	D-ARGININE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:139 , TYR A:140 , ARG B:7 , ASN B:66 , THR B:71 , TRP B:72 , GLY B:149 , ASP D:68	BINDING SITE FOR RESIDUE DAR B 165

(no "SS Bond" information available for 3KO9)

Asymmetric Unit

No.	Residues
1	Gly A:149	-	Pro A:150
2	Gly B:149	-	Pro B:150
3	Asn C:23	-	Glu C:24
4	Lys C:25	-	Glu C:26
5	Gly C:149	-	Pro C:150
6	Gly D:149	-	Pro D:150
7	Gly E:149	-	Pro E:150
8	Asp E:159	-	Ile E:160
9	Gly F:149	-	Pro F:150

(no "SAP(SNP)/Variant" information available for 3KO9)

(no "PROSITE Motif" information available for 3KO9)

(no "Exon" information available for 3KO9)

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:149
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains d3ko9a_ A: autom          ated matches                                                                                                                          SCOP domains
               CATH domains 3ko9A00 A:1-159            [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... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko9 A   1 MRVVIQRVKGAILSVR----------LEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10     |   -      | 30        40        50        60        70        80        90       100       110       120       130       140       150         
                                          16         27

Chain B 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 d3ko9b_ B: autom         ated matches                                                                                                                            SCOP domains
               CATH domains 3ko9B00 B: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.hhhhh..............hhhhhhhhhhhhhhhhhhh.hhh.eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko9 B   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160
                                          16        26

Chain C from PDB  Type:PROTEIN  Length:159
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains d3ko9c_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains 3ko9C00 C:1-159  [code=3.50.80.10, no name defined]                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee............eeeeee..eeeeeee.....hhhhhhhhhhhhhhheee........ee......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko9 C   1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains d3ko9d_ D: automa        ted matches                                                                                                                            SCOP domains
               CATH domains 3ko9D00 D:1-159          [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... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko9 D   1 MRVVIQRVKGAILSVRK--------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10      |  -     |  30        40        50        60        70        80        90       100       110       120       130       140       150         
                                           17       26

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 d3ko9e_ E: autom          ated matches                                                                                                                           SCOP domains
               CATH domains 3ko9E00 E: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.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko9 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:150
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains d3ko9f_ F: autom         ated matches                                                                                                                           SCOP domains
               CATH domains 3ko9F00 F:1-159           [code=3.50.80.10, no name defined]                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.---------..eeeeee..eeeeeee.....hhhhhhhhhhhhhhheeeee..eeeeee......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhh.....eee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ko9 F   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150         
                                          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	d3ko9a_	A:
1b	d3ko9b_	B:
1c	d3ko9c_	C:
1d	d3ko9d_	D:
1e	d3ko9e_	E:
1f	d3ko9f_	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	3ko9B00	B:1-160
1b	3ko9D00	D:1-159
1c	3ko9E00	E:1-160
1d	3ko9F00	F:1-159
1e	3ko9A00	A:1-159
1f	3ko9C00	C:1-159

(no "Pfam Domain" information available for 3KO9)

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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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn C:23 - Glu C:24	[ RasMol ]
		Asp E:159 - Ile E:160	[ RasMol ]
		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 ]
		Lys C:25 - Glu C:26	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	3ko9
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	3.1.-.-
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 6)

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Gene Ontology (9, 9)

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