3DKV - JenaLib

Title :   CRYSTAL STRUCTURE OF ADENYLATE KINASE VARIANT AKLSE1

Authors :   R. M. Bannen, C. M. Bianchetti, C. A. Bingman, E. B. Bitto

Date :   26 Jun 08 (Deposition) - 09 Jun 09 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

Chains :   Asym./Biol. Unit : A

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

Reference :   R. M. Bannen, E. Bae, J. G. Mccoy, G. N. Phillips Jr.
Crystal Structure Of Adenylate Kinase Variant Aklse1.
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

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 218
2	AC2	SOFTWARE	HOH A:227 , HOH A:238	BINDING SITE FOR RESIDUE MG A 219
3	AC3	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 , THR A:64 , GLY A:85 , PHE A:86 , ARG A:88 , GLN A:92 , ARG A:123 , LEU A:124 , ARG A:127 , THR A:136 , TYR A:137 , HIS A:138 , PHE A:141 , ARG A:160 , ARG A:171 , GLY A:197 , GLN A:199 , ILE A:201 , HOH A:226 , HOH A:228 , HOH A:238 , HOH A:261 , HOH A:272 , HOH A:273 , HOH A:275 , HOH A:293 , HOH A:317 , HOH A:396	BINDING SITE FOR RESIDUE AP5 A 220
4	AC4	SOFTWARE	PHE A:141 , ASP A:200 , ILE A:201 , HOH A:353	BINDING SITE FOR RESIDUE EDO A 221
5	AC5	SOFTWARE	HIS A:28 , ILE A:29 , SER A:30 , MET A:34 , ARG A:71 , HOH A:244	BINDING SITE FOR RESIDUE EDO A 222
6	AC6	SOFTWARE	GLY A:14 , SER A:30 , ASP A:33 , ARG A:36 , ASP A:84 , ARG A:160 , HOH A:416	BINDING SITE FOR RESIDUE EDO A 223

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
            KAD_BACSU     1 MNLVLMGLPGAGKGTQGERIVEDYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVKERLGKDDCERGFLLDGFPRTVAQAEALEEILEEYGKPIDYVINIEVDKDVLMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVSKRLEVNMKQTQPLLDFYSEKGYLANVNGQQDIQDVYADVKDLLGGLKK 217
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dkvA00 A:1-217 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhheeee.....eee..................ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ADENYLATE_KI----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dkv A   1 MNIVLMGLPGAGKGTQAERIVEKYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVRERLSKSDCERGFLLDGFPRTVAQAEALEEILEEMGRPIDYVINIQVDKEELMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVTKRLEVNMKQTAPLLAFYDSKEVLVNVNGQQDIQDVFADVKVILGGLKQ 217
                                    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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

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