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Title :   STRUCTURE OF BURKHOLDERIA THAILANDENSIS NUCLEOSIDE KINASE (BTHNK) IN COMPLEX WITH ADP-MIZORIBINE

Authors :   Y. Yasutake, H. Ota, E. Hino, S. Sakasegawa, T. Tamura

Date :   05 Jul 11 (Deposition) - 02 Nov 11 (Release) - 18 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym./Biol. Unit : A,B

Keywords :   Rossmann Fold, Kinase, Atp Binding, Mg Binding, Nucleoside Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Yasutake, H. Ota, E. Hino, S. Sakasegawa, T. Tamura
Structures Of Burkholderia Thailandensis Nucleoside Kinase: Implications For The Catalytic Mechanism And Nucleoside Selectivity
Acta Crystallogr. , Sect. D V. 67 945 2011
PubMed-ID: 22101821 | Reference-DOI: 10.1107/S0907444911038777

Molecule 1 - RIBOKINASE, PUTATIVE
	Chains	:	A, B
	EC Number	:	2.7.1.143
	Engineered	:	YES
	Expression System	:	RHODOCOCCUS ERYTHROPOLIS
	Expression System Plasmid	:	PTIP-QC2
	Expression System Strain	:	L88
	Expression System Taxid	:	1833
	Expression System Vector Type	:	PLASMID
	Gene	:	BTH_I1158
	Organism Scientific	:	BURKHOLDERIA THAILANDENSIS
	Organism Taxid	:	271848
	Strain	:	E264
	Synonym	:	NUCLEOSIDE KINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MZR	2	Ligand/Ion	5-HYDROXY-1-(BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE-4-CARBOXAMIDE
4	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:8 , ALA A:10 , ASP A:12 , GLY A:47 , GLY A:48 , CYS A:49 , ASN A:52 , PHE A:117 , GLN A:169 , ASP A:253 , HOH A:415 , HOH A:435 , HOH A:617 , SER B:36	BINDING SITE FOR RESIDUE MZR A 401
2	AC2	SOFTWARE	ASN A:111 , ASN A:192 , THR A:220 , ARG A:221 , GLY A:222 , GLU A:223 , GLY A:225 , VAL A:240 , CYS A:251 , GLY A:252 , SER A:277 , GLY A:280 , ILE A:284 , HOH A:327 , HOH A:349 , HOH A:353 , HOH A:366 , HOH A:380 , HOH A:415 , HOH A:424 , HOH A:446 , HOH A:482 , HOH A:494 , HIS B:31	BINDING SITE FOR RESIDUE ADP A 402
3	AC3	SOFTWARE	ILE A:183 , GLU A:184 , ALA A:186 , ARG A:213 , HOH A:392	BINDING SITE FOR RESIDUE NA A 403
4	AC4	SOFTWARE	SER A:36 , SER B:8 , ALA B:10 , ASP B:12 , GLY B:47 , GLY B:48 , CYS B:49 , ASN B:52 , PHE B:117 , GLN B:169 , ASP B:253 , HOH B:440 , HOH B:483	BINDING SITE FOR RESIDUE MZR B 401
5	AC5	SOFTWARE	HIS A:31 , ASN B:111 , ASN B:192 , THR B:220 , ARG B:221 , GLY B:222 , GLU B:223 , GLY B:225 , VAL B:240 , CYS B:251 , GLY B:252 , SER B:277 , GLY B:280 , ILE B:284 , HOH B:349 , HOH B:352 , HOH B:361 , HOH B:390 , HOH B:442 , HOH B:448 , HOH B:459 , HOH B:469 , HOH B:553 , HOH B:564	BINDING SITE FOR RESIDUE ADP B 402
6	AC6	SOFTWARE	ILE B:183 , GLU B:184 , ALA B:186 , ARG B:213 , VAL B:214 , HOH B:552	BINDING SITE FOR RESIDUE NA B 403
7	AC7	SOFTWARE	ARG B:20 , ARG B:22 , GLN B:124 , HIS B:126 , HOH B:378 , HOH B:394	BINDING SITE FOR RESIDUE GOL B 327

(no "SS Bond" information available for 3B1N)

(no "Cis Peptide Bond" information available for 3B1N)

(no "SAP(SNP)/Variant" information available for 3B1N)

(no "PROSITE Motif" information available for 3B1N)

(no "Exon" information available for 3B1N)

Asymmetric/Biological 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:311
 aligned with Q2SZE4_BURTA | Q2SZE4 from UniProtKB/TrEMBL  Length:312

    Alignment length:311
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 
         Q2SZE4_BURTA     2 ATLICGSIAYDNIMTFEGRFREHILPDQVHLINLSFLVPTMRREFGGCAGNIAYALNLLGGDARMMGTLGAVDAQPYLDRMDALGLSREYVRVLPDTYSAQAMITTDLDNNQITAFHPGAMMQSHVNHAGEAKDIKLAIVGPDGFQGMVQHTEELAQAGVPFIFDPGQGLPLFDGATLRRSIELATYIAVNDYEAKLVCDKTGWSEDEIASRVQALIITRGEHGATIRHRDGTEQIPAVRAERVIDPTGCGDAFRGGLLYGIEHGFDWATAGRLASLMGALKIAHQGPQTYAPTRAEIDARFETAFGYRPK 312
               SCOP domains d3b1na_ A: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeee...hhhhhh........eeeee......eeehhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhh.eeeeeeee.....eeeeeee......eeeeehhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh.hhhhhhh...eeeee.hhh.eeeee..eeeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b1n A   2 ATLICGSIAYDNIMTFEGRFREHILPDQVHLINLSFLVPTMRREFGGCAGNIAYALNLLGGDARMMGTLGAVDAQPYLDRMDALGLSREYVRVLPDTYSAQAMITTDLDNNQITAFHPGAMMQSHVNHAGEAKDIKLAIVGPDGFQGMVQHTEELAQAGVPFIFDPGQGLPLFDGATLRRSIELATYIAVNDYEAKLVCDKTGWSEDEIASRVQALIITRGEHGATIRHRDGTEQIPAVRAERVIDPTGCGDAFRGGLLYGIEHGFDWATAGRLASLMGALKIAHQGPQTYAPTRAEIDARFETAFGYRPK 312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain B from PDB  Type:PROTEIN  Length:320
 aligned with Q2SZE4_BURTA | Q2SZE4 from UniProtKB/TrEMBL  Length:312

    Alignment length:320
                                                                                                                                                                                                                                                                                                                                                312         
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311|        -
         Q2SZE4_BURTA     2 ATLICGSIAYDNIMTFEGRFREHILPDQVHLINLSFLVPTMRREFGGCAGNIAYALNLLGGDARMMGTLGAVDAQPYLDRMDALGLSREYVRVLPDTYSAQAMITTDLDNNQITAFHPGAMMQSHVNHAGEAKDIKLAIVGPDGFQGMVQHTEELAQAGVPFIFDPGQGLPLFDGATLRRSIELATYIAVNDYEAKLVCDKTGWSEDEIASRVQALIITRGEHGATIRHRDGTEQIPAVRAERVIDPTGCGDAFRGGLLYGIEHGFDWATAGRLASLMGALKIAHQGPQTYAPTRAEIDARFETAFGYRPK---------   -
               SCOP domains d3b1nb_ B: automated matches                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeee...hhhhh..........eeee......eeehhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhh.eeeeeeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh.hhhhhhh...eeeee.hhh.eeeee..eeeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b1n B   2 ATLICGSIAYDNIMTFEGRFREHILPDQVHLINLSFLVPTMRREFGGCAGNIAYALNLLGGDARMMGTLGAVDAQPYLDRMDALGLSREYVRVLPDTYSAQAMITTDLDNNQITAFHPGAMMQSHVNHAGEAKDIKLAIVGPDGFQGMVQHTEELAQAGVPFIFDPGQGLPLFDGATLRRSIELATYIAVNDYEAKLVCDKTGWSEDEIASRVQALIITRGEHGATIRHRDGTEQIPAVRAERVIDPTGCGDAFRGGLLYGIEHGFDWATAGRLASLMGALKIAHQGPQTYAPTRAEIDARFETAFGYRPKGSKLRSLEH 321
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: automated matches (88)

Protein domain: automated matches (88)

Burkholderia thailandensis [TaxId: 271848] (5)

1a	d3b1na_	A:
1b	d3b1nb_	B:

(no "CATH Domain" information available for 3B1N)

(no "Pfam Domain" information available for 3B1N)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q2SZE4_BURTA | Q2SZE4)

molecular function
	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:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	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: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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3b1n)

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	3b1n
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	2.7.1.143
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	Q2SZE4_BURTA \| Q2SZE4	:	3b1o 3b1p 3b1q 3b1r

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (5, 5)

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