1P72 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF EHV4-TK COMPLEXED WITH THY AND ADP

Authors :   A. Gardberg, L. Shuvalova, C. Monnerjahn, M. Konrad, A. Lavie

Date :   30 Apr 03 (Deposition) - 04 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (2x),B (2x)
Biol. Unit 3: A,B  (2x)
Biol. Unit 4: A (2x),B (2x)

Keywords :   P-Loop, Lid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Gardberg, L. Shuvalova, C. Monnerjahn, M. Konrad, A. Lavie
Structural Basis For The Dual Thymidine And Thymidylate Kinase Activity Of Herpes Thymidine Kinases.
Structure V. 11 1265 2003
PubMed-ID: 14527394 | Reference-DOI: 10.1016/J.STR.2003.09.003
(for further references see the PDB file header)

Molecule 1 - THYMIDINE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUT699
	Expression System Strain	:	BL21 C41 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TK
	Organism Common	:	EQUINE HERPESVIRUS 4
	Organism Scientific	:	EQUID HERPESVIRUS 4
	Organism Taxid	:	10331
	Strain	:	1942

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	SO4	9	Ligand/Ion	SULFATE ION
3	THM	2	Ligand/Ion	THYMIDINE

Biological Unit 1 (3, 13)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	SO4	9	Ligand/Ion	SULFATE ION
3	THM	2	Ligand/Ion	THYMIDINE

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	SO4	8	Ligand/Ion	SULFATE ION
3	THM	2	Ligand/Ion	THYMIDINE

Biological Unit 3 (3, 26)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	SO4	18	Ligand/Ion	SULFATE ION
3	THM	4	Ligand/Ion	THYMIDINE

Biological Unit 4 (3, 12)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	SO4	8	Ligand/Ion	SULFATE ION
3	THM	2	Ligand/Ion	THYMIDINE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:69 , GLU A:70 , THR A:71 , ARG A:104 , HOH A:846 , HOH A:881 , SER B:159	BINDING SITE FOR RESIDUE SO4 A 801
02	AC2	SOFTWARE	SER A:159 , HOH A:847 , PHE B:69 , GLU B:70 , THR B:71 , ARG B:104 , HOH B:873 , HOH B:963	BINDING SITE FOR RESIDUE SO4 B 802
03	AC3	SOFTWARE	ARG A:172 , PRO A:174 , GLN A:175	BINDING SITE FOR RESIDUE SO4 A 803
04	AC4	SOFTWARE	GLN A:202 , LEU B:125 , ARG B:127	BINDING SITE FOR RESIDUE SO4 A 804
05	AC5	SOFTWARE	ARG A:313 , GLN A:314	BINDING SITE FOR RESIDUE SO4 A 805
06	AC6	SOFTWARE	ARG A:172 , HOH A:937 , ARG B:172	BINDING SITE FOR RESIDUE SO4 A 806
07	AC7	SOFTWARE	ARG B:172 , PRO B:174 , GLN B:175	BINDING SITE FOR RESIDUE SO4 B 807
08	AC8	SOFTWARE	THR B:311 , HOH B:861	BINDING SITE FOR RESIDUE SO4 B 808
09	AC9	SOFTWARE	THR A:129 , GLN A:130 , ARG B:194	BINDING SITE FOR RESIDUE SO4 B 809
10	BC1	SOFTWARE	VAL A:33 , TYR A:34 , GLY A:35 , ILE A:36 , GLY A:37 , LYS A:38 , SER A:39 , THR A:40 , ARG A:192 , ARG A:196 , GLY A:310 , THR A:311 , PRO A:312 , CYS A:315 , HOH A:809 , HOH A:819 , HOH A:829 , HOH A:852 , HOH A:870 , HOH A:900 , HOH A:906 , HOH A:1030	BINDING SITE FOR RESIDUE ADP A 501
11	BC2	SOFTWARE	TYR A:34 , GLU A:60 , ILE A:74 , TYR A:78 , GLN A:102 , PHE A:105 , ARG A:139 , SER A:144 , PHE A:148 , HOH A:872 , HOH A:957	BINDING SITE FOR RESIDUE THM A 701
12	BC3	SOFTWARE	TYR B:34 , GLY B:35 , ILE B:36 , GLY B:37 , LYS B:38 , SER B:39 , THR B:40 , ARG B:192 , THR B:195 , ARG B:196 , GLY B:310 , THR B:311 , PRO B:312 , CYS B:315 , HOH B:815 , HOH B:823 , HOH B:855 , HOH B:912	BINDING SITE FOR RESIDUE ADP B 502
13	BC4	SOFTWARE	TYR B:34 , GLU B:60 , ILE B:74 , GLN B:102 , PHE B:105 , SER B:144 , PHE B:148 , GLU B:201 , HOH B:827 , HOH B:893 , HOH B:925	BINDING SITE FOR RESIDUE THM B 702

(no "SS Bond" information available for 1P72)

(no "Cis Peptide Bond" information available for 1P72)

(no "SAP(SNP)/Variant" information available for 1P72)

(no "PROSITE Motif" information available for 1P72)

(no "Exon" information available for 1P72)

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
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Chain A from PDB  Type:PROTEIN  Length:323
 aligned with KITH_EHV4 | P24425 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:333
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   
            KITH_EHV4    20 RRQVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRARIGEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMGV 352
               SCOP domains d1p72a_ A: Thymidine kinase                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1p72A00 A:20-352 P-loop containing nucleotide triphosphate hydr          olases                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.....hhhhhhhhhhhhhhh...eeee..hhhhhhh....hhhhhhhhhhh----------hhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......eeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhh........eeeeeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh..........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p72 A  20 SHMVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFETDVISGIYDTQN----------DAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRARIGEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMGV 352
                                    29        39        49        59        69        79  |      -   |    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   
                                                                                         82         93

Chain B from PDB  Type:PROTEIN  Length:330
 aligned with KITH_EHV4 | P24425 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:333
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   
            KITH_EHV4    20 RRQVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRARIGEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMGV 352
               SCOP domains d1p72b_ B: Thymidine kinase                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1p72B00 B:20-352 P-loop contain   ing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ------------Herpes_TK-1p72B01 B   :32-309                                                                                                                                                                                                                                                         ------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------Herpes_TK-1p72B02 B   :32-309                                                                                                                                                                                                                                                         ------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhh...---.eeee..hhhhhhh....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......eeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhh........eeeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p72 B  20 SHMVTIVRIYLDGVYGIGKSTTGRVMASAAS---PTLYFPEPMAYWRTLFETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRARIGEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMGV 352
                                    29        39        49|   |   59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   
                                                         50  54

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nucleotide and nucleoside kinases (231)

Protein domain: Thymidine kinase (34)

Equine herpesvirus type 4 [TaxId: 10331] (4)

1a	d1p72a_	A:
1b	d1p72b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Equine herpesvirus 4 (Equid herpesvirus 4) (4)

1a	1p72A00	A:20-352
1b	1p72B00	B:20-352

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Herpes_TK (18)

Equine herpesvirus 4 (strain 1942) (EHV-4) (Equine rhinopneumonitis virus) (4)

1a	Herpes_TK-1p72B01	B:32-309
1b	Herpes_TK-1p72B02	B:32-309

Asymmetric Unit(hide GO term definitions)

Chain A,B (KITH_EHV4 | P24425)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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.
	GO:0004797	thymidine kinase activity	Catalysis of the reaction: ATP + thymidine = ADP + thymidine 5'-phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006230	TMP biosynthetic process	The chemical reactions and pathways resulting in the formation of TMP, ribosylthymine monophosphate.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

Asymmetric Unit
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	Cis Peptide Bonds
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	1p72
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	KITH_EHV4 \| P24425
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	2.7.1.21
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	KITH_EHV4 \| P24425
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UniProtKB/Swiss-Prot
	KITH_EHV4 \| P24425	:	1p6x 1p73 1p75

1p6x	EHV4-TK COMPLEXED WITH THY AND SO4
1p73	EHV4-TK COMPLEXED WITH TP4A
1p75	EHV4-TK COMPLEXED WITH TP5A
1p7c	HSV1-TK COMPLEXED WITH TP5A

Description

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Ligands, Modified Residues, Ions (3, 13)

Sites (13, 13)

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