2OKV - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   C-MYC DNA UNWINDING ELEMENT BINDING PROTEIN

Authors :   B. Bae, S. K. Nair

Date :   17 Jan 07 (Deposition) - 30 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Dna Replication, Due, Atpase, Trna Deacylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kemp, B. Bae, J. P. Yu, M. Ghosh, M. Leffak, S. K. Nair
Structure And Function Of The C-Myc Dna-Unwinding Element-Binding Protein Due-B.
J. Biol. Chem. V. 282 10441 2007
PubMed-ID: 17264083 | Reference-DOI: 10.1074/JBC.M609632200

Molecule 1 - PROBABLE D-TYROSYL-TRNA(TYR) DEACYLASE 1
	Chains	:	A, B, C, D
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	HARS2, C20ORF88
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DNA UNWINDING ELEMENT BINDING PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:4 , GLN A:6 , CYS A:28 , LEU A:30	BINDING SITE FOR RESIDUE MG A 1201
2	AC2	SOFTWARE	VAL C:4 , GLN C:6 , CYS C:28 , LEU C:30	BINDING SITE FOR RESIDUE MG C 1202
3	AC3	SOFTWARE	VAL B:4 , GLN B:6 , CYS B:28 , LEU B:30	BINDING SITE FOR RESIDUE MG B 1203
4	AC4	SOFTWARE	VAL D:4 , GLN D:6 , CYS D:28 , LEU D:30	BINDING SITE FOR RESIDUE MG D 1204

(no "SS Bond" information available for 2OKV)

Asymmetric Unit

No.	Residues
1	Gly A:139	-	Pro A:140
2	Gly B:139	-	Pro B:140
3	Pro C:91	-	Asp C:92
4	Gly C:139	-	Pro C:140
5	Gly D:139	-	Pro D:140

(no "SAP(SNP)/Variant" information available for 2OKV)

(no "PROSITE Motif" information available for 2OKV)

Asymmetric Unit (4, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000377452	1a	ENSE00001473997	chr20:18568537-18568759	223	DTD1_HUMAN	1-15	15	4	A:1-15 B:1-15 C:1-15 D:1-15	15 15 15 15
1.2	ENST00000377452	2	ENSE00001102946	chr20:18574375-18574465	91	DTD1_HUMAN	15-45	31	4	A:15-45 B:15-45 C:15-45 D:15-45	31 31 31 31
1.3	ENST00000377452	3	ENSE00000660176	chr20:18576650-18576885	236	DTD1_HUMAN	45-124	80	4	A:45-124 B:45-124 C:45-124 D:45-124	80 80 80 80
1.4	ENST00000377452	4	ENSE00000660178	chr20:18608771-18608877	107	DTD1_HUMAN	124-159	36	4	A:124-149 B:124-150 C:124-149 D:124-149	26 27 26 26
1.6	ENST00000377452	6	ENSE00001162838	chr20:18724744-18724915	172	DTD1_HUMAN	160-209	50	0	-	-
1.7	ENST00000377452	7	ENSE00001473954	chr20:18744004-18744561	558	DTD1_HUMAN	-	0	0	-	-

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 DTD1_HUMAN | Q8TEA8 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
           DTD1_HUMAN     1 MKAVVQRVTRASVTVGGEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDKQYEILCVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHIQNDGPVTIELESPA 149
               SCOP domains d2okva_ A: automated matches                                                                                                                          SCOP domains
               CATH domains 2okvA00 A:1-149  [code=3.50.80.10, no name defined]                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh.............hhhhhh.eeeeee.hhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      -----------------------------Exon 1.3  PDB: A:45-124 UniProt: 45-124                                         ------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.2  PDB: A:15-45         ------------------------------------------------------------------------------Exon 1.4  PDB: A:124-149   Transcript 1 (2)
                 2okv A   1 MKAVVQRVTRASVTVGGEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDKQYEILCVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHIQNDGPVTIELESPA 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with DTD1_HUMAN | Q8TEA8 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
           DTD1_HUMAN     1 MKAVVQRVTRASVTVGGEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDKQYEILCVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHIQNDGPVTIELESPAP 150
               SCOP domains d2okvb_ B: automated matches                                                                                                                           SCOP domains
               CATH domains 2okvB00 B:1-150  [code=3.50.80.10, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeee..eeeeeee.....hhhhhhhhhhhhhhheee.........eehhhhh.eeeeee.hhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a      -----------------------------Exon 1.3  PDB: B:45-124 UniProt: 45-124                                         -------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.2  PDB: B:15-45         ------------------------------------------------------------------------------Exon 1.4  PDB: B:124-150    Transcript 1 (2)
                 2okv B   1 MKAVVQRVTRASVTVGGEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDKQYEILCVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHIQNDGPVTIELESPAP 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with DTD1_HUMAN | Q8TEA8 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
           DTD1_HUMAN     1 MKAVVQRVTRASVTVGGEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDKQYEILCVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHIQNDGPVTIELESPA 149
               SCOP domains d2okvc_ C: automated matches                                                                                                                          SCOP domains
               CATH domains 2okvC00 C:1-149  [code=3.50.80.10, no name defined]                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh.............hhhhhh.eeeeee.hhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      -----------------------------Exon 1.3  PDB: C:45-124 UniProt: 45-124                                         ------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.2  PDB: C:15-45         ------------------------------------------------------------------------------Exon 1.4  PDB: C:124-149   Transcript 1 (2)
                 2okv C   1 MKAVVQRVTRASVTVGGEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDKQYEILCVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHIQNDGPVTIELESPA 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:149
 aligned with DTD1_HUMAN | Q8TEA8 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
           DTD1_HUMAN     1 MKAVVQRVTRASVTVGGEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDKQYEILCVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHIQNDGPVTIELESPA 149
               SCOP domains d2okvd_ D: automated matches                                                                                                                          SCOP domains
               CATH domains 2okvD00 D:1-149  [code=3.50.80.10, no name defined]                                                                                                   CATH domains
           Pfam domains (1) -Tyr_Deacylase-2okvD01 D:2-147                                                                                                                     -- Pfam domains (1)
           Pfam domains (2) -Tyr_Deacylase-2okvD02 D:2-147                                                                                                                     -- Pfam domains (2)
           Pfam domains (3) -Tyr_Deacylase-2okvD03 D:2-147                                                                                                                     -- Pfam domains (3)
           Pfam domains (4) -Tyr_Deacylase-2okvD04 D:2-147                                                                                                                     -- Pfam domains (4)
         Sec.struct. author .eeeeeeeeeeeeee..eeeeee..eeeeeee.....hhhhhhhhhhhhhhheee.........eehhhhh.eeeeee.hhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      -----------------------------Exon 1.3  PDB: D:45-124 UniProt: 45-124                                         ------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.2  PDB: D:15-45         ------------------------------------------------------------------------------Exon 1.4  PDB: D:124-149   Transcript 1 (2)
                 2okv D   1 MKAVVQRVTRASVTVGGEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDKQYEILCVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHIQNDGPVTIELESPA 149
                                    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)
		→ 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)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2okva_	A:
1b	d2okvb_	B:
1c	d2okvc_	C:
1d	d2okvd_	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)

Human (Homo sapiens) (1)

1a	2okvB00	B:1-150
1b	2okvA00	A:1-149
1c	2okvC00	C:1-149
1d	2okvD00	D:1-149

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Tyr_Deacylase (12)

Homo sapiens (Human) (1)

1a	Tyr_Deacylase-2okvD01	D:2-147
1b	Tyr_Deacylase-2okvD02	D:2-147
1c	Tyr_Deacylase-2okvD03	D:2-147
1d	Tyr_Deacylase-2okvD04	D:2-147

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DTD1_HUMAN | Q8TEA8)

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:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	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.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:139 - Pro A:140	[ RasMol ]
		Gly B:139 - Pro B:140	[ RasMol ]
		Gly C:139 - Pro C:140	[ RasMol ]
		Gly D:139 - Pro D:140	[ RasMol ]
		Pro C:91 - Asp C:92	[ RasMol ]

Biological Units
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Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

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Exons (4, 16)

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