3HPR - JenaLib

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Title :   CRYSTAL STRUCTURE OF V148G ADENYLATE KINASE FROM E. COLI, IN COMPLEX WITH AP5A

Authors :   V. J. Hilser, T. P. Travis, D. W. Bolen

Date :   04 Jun 09 (Deposition) - 03 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Enzyme Inhibitor Complex, Atp-Binding, Kinase, Nucleotide Biosynthesis, Nucleotide-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. P. Schrank, D. W. Bolen, V. J. Hilser
Rational Modulation Of Conformational Fluctuations In Adenylate Kinase Reveals A Local Unfolding Mechanism For Allostery And Functional Adaptation In Proteins.
Proc. Natl. Acad. Sci. Usa V. 106 16984 2009
PubMed-ID: 19805185 | Reference-DOI: 10.1073/PNAS.0906510106

Molecule 1 - ADENYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEAK91V148G
	Expression System Strain	:	HMS174
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ADK, B0474, DNAW, JW0463, PLSA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	AK, ATP-AMP TRANSPHOSPHORYLASE

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	AP5	2	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	AP5	1	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AP5	1	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	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 , LEU A:35 , ARG A:36 , MET A:53 , LYS A:57 , VAL A:59 , VAL A:64 , GLY A:85 , PHE A:86 , ARG A:88 , GLN A:92 , ARG A:119 , ARG A:123 , VAL A:132 , TYR A:133 , HIS A:134 , PHE A:137 , ARG A:156 , ASP A:158 , ARG A:167 , GLY A:198 , LYS A:200 , VAL A:202 , HOH A:216 , HOH A:218 , HOH A:230 , HOH A:235 , HOH A:240 , HOH A:245 , HOH A:278 , HOH A:308 , HOH A:333 , HOH A:357 , HOH A:358 , HOH A:434 , HOH A:437	BINDING SITE FOR RESIDUE AP5 A 215
2	AC2	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 , LEU B:35 , ARG B:36 , MET B:53 , LYS B:57 , VAL B:59 , GLU B:62 , VAL B:64 , GLY B:85 , ARG B:88 , GLN B:92 , ARG B:119 , ARG B:123 , VAL B:132 , TYR B:133 , HIS B:134 , PHE B:137 , ARG B:156 , ARG B:167 , LYS B:200 , VAL B:202 , HOH B:224 , HOH B:231 , HOH B:238 , HOH B:239 , HOH B:275 , HOH B:294 , HOH B:351	BINDING SITE FOR RESIDUE AP5 B 215

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

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 3HPR)

Asymmetric Unit (1, 2)

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

(no "Exon" information available for 3HPR)

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:214
 aligned with KAD_ECOLI | P69441 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
            KAD_ECOLI     1 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG 214
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhh..eeehhhhhhhhhhhh.....hhhhhhhh....hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh.....eeeeee.hhhhhhhhhhheee......eee.........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ADENYLATE_KI-------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hpr A   1 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDGTGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG 214
                                    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:214
 aligned with KAD_ECOLI | P69441 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
            KAD_ECOLI     1 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG 214
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhh..eeehhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh....eeeeee.hhhhhhhhhhheee......eee.........................hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ADENYLATE_KI-------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hpr B   1 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDGTGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG 214
                                    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 3HPR)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (KAD_ECOLI | P69441)

molecular function
	GO:0016208	AMP binding	Interacting selectively and non-covalently with AMP, adenosine monophosphate.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0006172	ADP biosynthetic process	The chemical reactions and pathways resulting in the formation of ADP, adenosine 5'-diphosphate.
	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:0032774	RNA biosynthetic process	The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
	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:0008654	phospholipid biosynthetic process	The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
	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.
	GO:0015951	purine ribonucleotide interconversion	The chemical reactions and pathways by which a purine ribonucleotide is synthesized from another purine ribonucleotide.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	3hpr
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	KAD_ECOLI \| P69441	:	1ake 1ank 1e4v 1e4y 2eck 3hpq 4ake 4x8h 4x8l 4x8m 4x8o 5eje

3hpq	CRYSTAL STRUCTURE OF WILD-TYPE ADENYLATE KINASE FROM E. COLI, IN COMPLEX WITH AP5A, SOLVED UNDER IDENTICAL CONDITIONS FOR COMPARISON

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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