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Title :   CRYSTAL STRUCTURE OF A THERMOSTABLE MUTANT OF BACILLUS SUBTILIS ADENYLATE KINASE (Q199R)

Authors :   S. Chen, Y. Shamoo

Date :   28 Oct 05 (Deposition) - 27 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Adenylate Kinase, Thermostability, Point Mutant, In Vivo Evolution, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Counago, S. Chen, Y. Shamoo
In Vivo Molecular Evolution Reveals Biophysical Origins Of Organismal Fitness.
Mol. Cell V. 22 441 2006
PubMed-ID: 16713575 | Reference-DOI: 10.1016/J.MOLCEL.2006.04.012
(for further references see the PDB file header)

Molecule 1 - ADENYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ADK
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	ATP-AMP TRANSPHOSPHORYLASE, AK, SUPEROXIDE- INDUCIBLE PROTEIN 16, SOI16

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	AP5	2	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE
2	CA	1	Ligand/Ion	CALCIUM ION
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	AP5	1	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AP5	1	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:130 , CYS A:133 , CYS A:150 , ASP A:153	BINDING SITE FOR RESIDUE ZN A 220
2	AC2	SOFTWARE	CYS B:130 , CYS B:133 , CYS B:150 , ASP B:153	BINDING SITE FOR RESIDUE ZN B 221
3	AC3	SOFTWARE	AP5 B:1219 , HOH B:1238 , HOH B:1239 , HOH B:1437 , HOH B:1439 , HOH B:1440	BINDING SITE FOR RESIDUE MG B 1222
4	AC4	SOFTWARE	AP5 A:1218 , HOH A:1228 , HOH A:1325 , HOH A:1427 , HOH A:1509	BINDING SITE FOR RESIDUE MG A 1223
5	AC5	SOFTWARE	GLY A:190 , HOH A:1281 , HOH A:1302 , ALA B:161 , ASN B:164 , HOH B:1245 , HOH B:1256	BINDING SITE FOR RESIDUE CA B 1223
6	AC6	SOFTWARE	PRO A:9 , GLY A:10 , ALA A:11 , GLY A:12 , LYS A:13 , GLY A:14 , THR A:15 , THR A:31 , GLY A:32 , ARG A:36 , ILE A:53 , GLU A:57 , VAL A:59 , GLY A:85 , PHE A:86 , ARG A:88 , GLN A:92 , ARG A:123 , ARG A:127 , THR A:136 , TYR A:137 , HIS A:138 , PHE A:141 , ARG A:160 , ARG A:171 , ARG A:199 , ILE A:201 , MG A:1223 , HOH A:1227 , HOH A:1228 , HOH A:1229 , HOH A:1230 , HOH A:1249 , HOH A:1273 , HOH A:1311 , HOH A:1318 , HOH A:1325 , HOH A:1509	BINDING SITE FOR RESIDUE AP5 A 1218
7	AC7	SOFTWARE	PRO B:9 , GLY B:10 , ALA B:11 , GLY B:12 , LYS B:13 , GLY B:14 , THR B:15 , THR B:31 , GLY B:32 , PHE B:35 , ARG B:36 , ILE B:53 , GLU B:57 , VAL B:59 , THR B:64 , GLY B:85 , PHE B:86 , ARG B:88 , GLN B:92 , ARG B:123 , ARG B:127 , THR B:136 , TYR B:137 , HIS B:138 , PHE B:141 , ARG B:160 , ARG B:171 , ARG B:199 , ILE B:201 , MG B:1222 , HOH B:1226 , HOH B:1231 , HOH B:1235 , HOH B:1238 , HOH B:1276 , HOH B:1290 , HOH B:1314 , HOH B:1439 , HOH B:1440 , HOH B:1441	BINDING SITE FOR RESIDUE AP5 B 1219

(no "SS Bond" information available for 2EU8)

Asymmetric Unit

No.	Residues
1	Phe A:86	-	Pro A:87
2	Phe B:86	-	Pro B:87

(no "SAP(SNP)/Variant" information available for 2EU8)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD_BACSU	81-92	2	A:81-92 B:81-92

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD_BACSU	81-92	1	A:81-92 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD_BACSU	81-92	1	- B:81-92

(no "Exon" information available for 2EU8)

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:216
 aligned with KAD_BACSU | P16304 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
            KAD_BACSU     1 MNLVLMGLPGAGKGTQGERIVEDYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVKERLGKDDCERGFLLDGFPRTVAQAEALEEILEEYGKPIDYVINIEVDKDVLMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVSKRLEVNMKQTQPLLDFYSEKGYLANVNGQQDIQDVYADVKDLLGGLK 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2eu8A00 A:1-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhheeee.....eee..................ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ADENYLATE_KI---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2eu8 A   1 MNLVLMGLPGAGKGTQGERIVEDYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVKERLGKDDCERGFLLDGFPRTVAQAEALEEILEEYGKPIDYVINIEVDKDVLMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVSKRLEVNMKQTQPLLDFYSEKGYLANVNGQRDIQDVYADVKDLLGGLK 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with KAD_BACSU | P16304 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
            KAD_BACSU     1 MNLVLMGLPGAGKGTQGERIVEDYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVKERLGKDDCERGFLLDGFPRTVAQAEALEEILEEYGKPIDYVINIEVDKDVLMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVSKRLEVNMKQTQPLLDFYSEKGYLANVNGQQDIQDVYADVKDLLGGLK 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2eu8B00 B:1-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhheeee.....eee..................ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ADENYLATE_KI---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2eu8 B   1 MNLVLMGLPGAGKGTQGERIVEDYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVKERLGKDDCERGFLLDGFPRTVAQAEALEEILEEYGKPIDYVINIEVDKDVLMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVSKRLEVNMKQTQPLLDFYSEKGYLANVNGQRDIQDVYADVKDLLGGLK 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

(no "SCOP Domain" information available for 2EU8)

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)

Bacillus subtilis. Organism_taxid: 1423. (11)

1a	2eu8A00	A:1-216
1b	2eu8B00	B:1-216

(no "Pfam Domain" information available for 2EU8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KAD_BACSU | P16304)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004017	adenylate kinase activity	Catalysis of the reaction: ATP + AMP = 2 ADP.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019205	nucleobase-containing compound kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate.
	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:0016776	phosphotransferase activity, phosphate group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a phosphate 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:0044209	AMP salvage	The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0046939	nucleotide phosphorylation	The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
	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.
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
		Phe A:86 - Pro A:87	[ RasMol ]
		Phe B:86 - Pro B:87	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	2.7.4.3
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	KAD_BACSU \| P16304	:	1p3j 2oo7 2ori 2osb 2p3s 2qaj 3dkv 3dl0 4mkf 4mkg 4mkh 4qbf 4qbg 4typ 4tyq

1p3j	CRYSTAL STRUCTURE OF WILD-TYPE ADENYLATE KINASE FROM BACILLUS SUBTILIS
1zin	CRYSTAL STRUCTURE OF WILD-TYPE ADENYLATE KINASE FROM GEOBACILLUS STEAROTHERMOPHILUS WITH BOUND AP5A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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