1KHT - JenaLib

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Title :   ADENYLATE KINASE FROM METHANOCOCCUS VOLTAE

Authors :   A. R. Criswell, J. Konisky, G. N. Phillips Jr.

Date :   30 Nov 01 (Deposition) - 03 Jun 03 (Release) - 28 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Kinase, Phosphotransferase, Signaling Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. R. Criswell, E. Bae, B. Stec, J. Konisky, G. N. Phillips Jr.
Structures Of Thermophilic And Mesophilic Adenylate Kinases From The Genus Methanococcus
J. Mol. Biol. V. 330 1087 2003
PubMed-ID: 12860130 | Reference-DOI: 10.1016/S0022-2836(03)00655-7

Molecule 1 - ADENYLATE KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.4.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ADK
	Organism Scientific	:	METHANOCOCCUS VOLTAE
	Organism Taxid	:	2188
	Synonym	:	ATP-AMP TRANSPHOSPHORYLASE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	AMP	4	Ligand/Ion	ADENOSINE MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE B:39 , GLY B:40 , MET B:43 , ARG B:56 , ARG B:60 , GLN B:71 , THR B:91 , HIS B:92 , VAL B:95 , GLY B:104 , ARG B:138 , HOH B:2197 , HOH B:2201 , HOH B:2274 , HOH B:2281	BINDING SITE FOR RESIDUE AMP B 2193
2	AC2	SOFTWARE	PHE C:39 , MET C:43 , ARG C:56 , ARG C:60 , GLN C:71 , THR C:91 , HIS C:92 , VAL C:95 , GLY C:104 , ARG C:138 , HOH C:3213 , HOH C:3214	BINDING SITE FOR RESIDUE AMP C 3193

(no "SS Bond" information available for 1KHT)

(no "Cis Peptide Bond" information available for 1KHT)

(no "SAP(SNP)/Variant" information available for 1KHT)

(no "PROSITE Motif" information available for 1KHT)

(no "Exon" information available for 1KHT)

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:190
 aligned with KADA_METVO | P43411 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:190
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
           KADA_METVO     3 NKVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSFGSVMFEVAKEENLVSDRDQMRKMDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVSTPKGYLPGLPSWVLNELNPDLIIVVETTGDEILMRRMSDETRVRDLDTASTIEQHQFMNRCAAMSYGVLTGATVKIVQNRNGLLDQAVEELTNVLR 192
               SCOP domains d1khta_ A: Adenylate kinase                                                                                                                                                                    SCOP domains
               CATH domains 1khtA00 A:3-192 P-loop containing nucleotide triphosphate hydrolases                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeee...eeee..eeee..hhhhhhhhh..eeeeee.hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kht A   3 NKVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSFGSVMFEVAKEENLVSDRDQMRKMDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVSTPKGYLPGLPSWVLNELNPDLIIVVETTGDEILMRRMSDETRVRDLDTASTIEQHQFMNRCAAMSYGVLTGATVKIVQNRNGLLDQAVEELTNVLR 192
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with KADA_METVO | P43411 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
           KADA_METVO     2 KNKVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSFGSVMFEVAKEENLVSDRDQMRKMDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVSTPKGYLPGLPSWVLNELNPDLIIVVETTGDEILMRRMSDETRVRDLDTASTIEQHQFMNRCAAMSYGVLTGATVKIVQNRNGLLDQAVEELTNVLR 192
               SCOP domains d1khtb_ B: Adenylate kinase                                                                                                                                                                     SCOP domains
               CATH domains 1khtB00 B:2-192 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeee..eeee..hhhhhhhhh..eeeeee.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kht B   2 KNKVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSFGSVMFEVAKEENLVSDRDQMRKMDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVSTPKGYLPGLPSWVLNELNPDLIIVVETTGDEILMRRMSDETRVRDLDTASTIEQHQFMNRCAAMSYGVLTGATVKIVQNRNGLLDQAVEELTNVLR 192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain C from PDB  Type:PROTEIN  Length:191
 aligned with KADA_METVO | P43411 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
           KADA_METVO     2 KNKVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSFGSVMFEVAKEENLVSDRDQMRKMDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVSTPKGYLPGLPSWVLNELNPDLIIVVETTGDEILMRRMSDETRVRDLDTASTIEQHQFMNRCAAMSYGVLTGATVKIVQNRNGLLDQAVEELTNVLR 192
               SCOP domains d1khtc_ C: Adenylate kinase                                                                                                                                                                     SCOP domains
               CATH domains 1khtC00 C:2-192 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
           Pfam domains (1) ----AAA_18-1khtC01 C:6-155                                                                                                                                ------------------------------------- Pfam domains (1)
           Pfam domains (2) ----AAA_18-1khtC02 C:6-155                                                                                                                                ------------------------------------- Pfam domains (2)
           Pfam domains (3) ----AAA_18-1khtC03 C:6-155                                                                                                                                ------------------------------------- Pfam domains (3)
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhh.....eeeehhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh....eeee...eeee..eeee..hhhhhhhhh..eeeeee.hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kht C   2 KNKVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSFGSVMFEVAKEENLVSDRDQMRKMDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVSTPKGYLPGLPSWVLNELNPDLIIVVETTGDEILMRRMSDETRVRDLDTASTIEQHQFMNRCAAMSYGVLTGATVKIVQNRNGLLDQAVEELTNVLR 192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nucleotide and nucleoside kinases (231)

Protein domain: Adenylate kinase (28)

Methanococcus voltae [TaxId: 2188] (1)

1a	d1khta_	A:
1b	d1khtb_	B:
1c	d1khtc_	C:

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)

Methanococcus voltae. Organism_taxid: 2188. (12)

1a	1khtB00	B:2-192
1b	1khtC00	C:2-192
1c	1khtA00	A:3-192

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: AAA_18 (7)

Methanococcus voltae (1)

1a	AAA_18-1khtC01	C:6-155
1b	AAA_18-1khtC02	C:6-155
1c	AAA_18-1khtC03	C:6-155

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (KADA_METVO | P43411)

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: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: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: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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Biological Units
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1ki9	ADENYLATE KINASE FROM METHANOCOCCUS THERMOLITHOTROPHICUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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, 3)

CATH Domains (1, 3)

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Gene Ontology (8, 8)

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Related Entries Specified in the PDB File