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Title :   STRUCTURE OF PHOSPHOTRANSFERASE

Authors :   M. B. Berry, T. Bilderback, M. Glaser, G. N. Phillips Jr.

Date :   16 Dec 96 (Deposition) - 12 Mar 97 (Release) - 13 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Transferase, Kinase, Atp-Binding, Phosphotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. B. Berry, E. Bae, T. R. Bilderback, M. Glaser, G. N. Phillips
Crystal Structure Of Adp/Amp Complex Of Escherichia Coli Adenylate Kinase.
Proteins V. 62 555 2006
PubMed-ID: 16302237 | Reference-DOI: 10.1002/PROT.20699
(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
	Expression System Gene	:	ADK+
	Expression System Plasmid	:	PLP101
	Expression System Taxid	:	562
	Gene	:	ADK+
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ADK

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:31 , LEU A:35 , ARG A:36 , LYS A:57 , VAL A:59 , GLY A:85 , ARG A:88 , GLN A:92 , ARG A:156 , HOH A:217	BINDING SITE FOR RESIDUE AMP A 215
2	AC2	SOFTWARE	GLY A:10 , ALA A:11 , GLY A:12 , LYS A:13 , GLY A:14 , THR A:15 , GLU A:62 , ARG A:119 , ARG A:123 , VAL A:132 , TYR A:133 , HIS A:134 , PHE A:137 , LYS A:200 , VAL A:202 , HOH A:221	BINDING SITE FOR RESIDUE ADP A 216
3	AC3	SOFTWARE	THR B:31 , LEU B:35 , ARG B:36 , MET B:53 , LYS B:57 , VAL B:59 , VAL B:64 , GLY B:85 , ARG B:88 , GLN B:92 , ARG B:156 , ASP B:158 , HOH B:217 , HOH B:223	BINDING SITE FOR RESIDUE AMP B 215
4	AC4	SOFTWARE	GLY B:10 , ALA B:11 , GLY B:12 , LYS B:13 , GLY B:14 , THR B:15 , GLU B:62 , ARG B:119 , ARG B:123 , VAL B:132 , TYR B:133 , HIS B:134 , PHE B:137 , LYS B:200 , VAL B:202 , HOH B:219	BINDING SITE FOR RESIDUE ADP B 216

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

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 2ECK)

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 2ECK)

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 d2ecka1 A:1-121,A:157-214 Adenylate kinase                                                                               d2ecka2 A:122-156                  d2ecka1 A:1-121,A:157-214 Adenylate kinase                 SCOP domains
               CATH domains 2eckA00 A:1-214 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh..eee.hhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhh.hhhh..eeee.....hhhhhhhhh......eeeeee..hhhhhhhhhheeee....eeee..........................hhhhhhhhhhhhhh.hhhhhhhhhhhhh...eeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ADENYLATE_KI-------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eck A   1 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG 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 d2eckb1 B:1-121,B:157-214 Adenylate kinase                                                                               d2eckb2 B:122-156                  d2eckb1 B:1-121,B:157-214 Adenylate kinase                 SCOP domains
               CATH domains 2eckB00 B:1-214 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh..eeeehhhhhhhhhhh.....hhhhhhh.......hhhhhhhhhhh....hhh..eeee.....hhhhhhhhh......eeeeee..hhhhhhhhhheeee....eeee..........................hhhhhhhhhhhhhh.hhhhhhhhhhhhh...eeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ADENYLATE_KI-------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eck B   1 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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	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(

)

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)

Escherichia coli. Organism_taxid: 562. (54)

1a	2eckA00	A:1-214
1b	2eckB00	B:1-214

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

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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