3H86 - JenaLib

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Title :   CRYSTAL STRUCTURE OF ADENYLATE KINASE FROM METHANOCOCCUS MARIPALUDIS

Authors :   D. G. Milya, S. Yousif

Date :   28 Apr 09 (Deposition) - 06 Oct 09 (Release) - 22 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,G
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: G  (3x)
Biol. Unit 3: A (3x),B (3x),C (3x),G (3x)

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

Reference :   M. Davlieva, Y. Shamoo
Crystal Structure Of A Trimeric Archaeal Adenylate Kinase From The Mesophile Methanococcus Maripaludis With An Unusually Broad Functional Range And Thermal Stability.
Proteins V. 78 357 2009
PubMed-ID: 19731371 | Reference-DOI: 10.1002/PROT.22549
(for further references see the PDB file header)

Molecule 1 - ADENYLATE KINASE
	Chains	:	B, A, C, G
	EC Number	:	2.7.4.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	ROSETTA 2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ADK, ADKA, MMP1031
	Organism Scientific	:	METHANOCOCCUS MARIPALUDIS
	Organism Taxid	:	39152
	Strain	:	ATCC 43000D
	Synonym	:	AK, ATP-AMP TRANSPHOSPHORYLASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	G
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (3x)	:				G
Biological Unit 3 (3x)	:	A (3x)	B (3x)	C (3x)	G (3x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	AP5	4	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	AP5	3	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	AP5	3	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE

Biological Unit 3 (0, 0)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO B:12 , GLY B:13 , GLY B:15 , GLY B:16 , THR B:17 , THR B:18 , PHE B:39 , GLY B:40 , MET B:43 , ARG B:56 , GLN B:71 , THR B:91 , HIS B:92 , VAL B:95 , GLY B:104 , ARG B:131 , ASP B:135 , ARG B:138 , ARG B:140 , ASN B:175 , LYS B:176 , ASN B:177 , GLY B:178	BINDING SITE FOR RESIDUE AP5 B 193
2	AC2	SOFTWARE	PRO A:12 , GLY A:13 , VAL A:14 , GLY A:15 , GLY A:16 , THR A:17 , THR A:18 , ASN A:38 , GLY A:40 , MET A:43 , ARG A:56 , ARG A:60 , GLN A:71 , THR A:91 , HIS A:92 , VAL A:95 , GLY A:104 , ARG A:131 , SER A:134 , ASP A:135 , ARG A:138 , ARG A:140 , ASN A:175 , LYS A:176 , GLY A:178 , VAL A:180 , HOH A:195	BINDING SITE FOR RESIDUE AP5 A 193
3	AC3	SOFTWARE	PRO C:12 , GLY C:13 , VAL C:14 , GLY C:15 , THR C:17 , THR C:18 , PHE C:39 , GLY C:40 , ARG C:56 , MET C:59 , ARG C:60 , GLN C:71 , THR C:91 , HIS C:92 , VAL C:95 , GLY C:104 , ARG C:131 , ASP C:135 , ARG C:138 , ARG C:140 , VAL C:180	BINDING SITE FOR RESIDUE AP5 C 193
4	AC4	SOFTWARE	PRO G:12 , GLY G:13 , VAL G:14 , GLY G:15 , GLY G:16 , THR G:17 , THR G:18 , ASN G:38 , PHE G:39 , GLY G:40 , MET G:43 , ARG G:56 , ARG G:60 , GLN G:71 , THR G:91 , HIS G:92 , GLY G:104 , ARG G:131 , ARG G:138 , ASN G:175 , LYS G:176 , ASN G:177 , GLY G:178 , HOH G:199	BINDING SITE FOR RESIDUE AP5 G 193

(no "SS Bond" information available for 3H86)

(no "Cis Peptide Bond" information available for 3H86)

(no "SAP(SNP)/Variant" information available for 3H86)

(no "PROSITE Motif" information available for 3H86)

(no "Exon" information available for 3H86)

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:191
 aligned with KADA_METMP | Q6LYG0 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_METMP     2 KNKVVVVTGVPGVGGTTVTQKAMDILSEEGLNYKMVNFGSAMFDVANEEGLASDRDQMRRLDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVKTPKGYLPGLPAWVLTELNPDIVIVVETDGDEILMRRLSDESRKRDLETTASIEEHQFMNRAAAMSYGVLTGATVKIVKNKNGLVDNAVEELMSVLR 192
               SCOP domains d3h86a_ A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains 3h86A00 A:2-192 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh.....eeeehhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhhh......eeeee..eeee..eeee..hhhhhhhhh..eeeeee.hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h86 A   2 KNKVVVVTGVPGVGGTTVTQKAMDILSEEGLNYKMVNFGSAMFDVANEEGLASDRDQMRKLDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVKTPKGYLPGLPAWVLTELNPDIVIVVETDGDEILMRRLSDESRKRDLETTASIEEHQFMNRAAAMSYGVLTGATVKIVKNKNGLVDNAVEELMSVLR 192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with KADA_METMP | Q6LYG0 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_METMP     2 KNKVVVVTGVPGVGGTTVTQKAMDILSEEGLNYKMVNFGSAMFDVANEEGLASDRDQMRRLDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVKTPKGYLPGLPAWVLTELNPDIVIVVETDGDEILMRRLSDESRKRDLETTASIEEHQFMNRAAAMSYGVLTGATVKIVKNKNGLVDNAVEELMSVLR 192
               SCOP domains d3h86b_ B: automated matches                                                                                                                                                                    SCOP domains
               CATH domains 3h86B00 B:2-192 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh......eeehhhhhhhhhhh................hhhhhhhhhhhhhhhhhhh..eeee...eeee..eeee..hhhhhhh....eeeeee.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h86 B   2 KNKVVVVTGVPGVGGTTVTQKAMDILSEEGLNYKMVNFGSAMFDVANEEGLASDRDQMRKLDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVKTPKGYLPGLPAWVLTELNPDIVIVVETDGDEILMRRLSDESRKRDLETTASIEEHQFMNRAAAMSYGVLTGATVKIVKNKNGLVDNAVEELMSVLR 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_METMP | Q6LYG0 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_METMP     2 KNKVVVVTGVPGVGGTTVTQKAMDILSEEGLNYKMVNFGSAMFDVANEEGLASDRDQMRRLDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVKTPKGYLPGLPAWVLTELNPDIVIVVETDGDEILMRRLSDESRKRDLETTASIEEHQFMNRAAAMSYGVLTGATVKIVKNKNGLVDNAVEELMSVLR 192
               SCOP domains d3h86c_ C: automated matches                                                                                                                                                                    SCOP domains
               CATH domains 3h86C00 C:2-192 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh........hhhhhh...hhhhh...........hhhhhh....hhhhhhhhhh....eeee...eeee..eeee..hhhhhhhhh..eeeeee.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h86 C   2 KNKVVVVTGVPGVGGTTVTQKAMDILSEEGLNYKMVNFGSAMFDVANEEGLASDRDQMRKLDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVKTPKGYLPGLPAWVLTELNPDIVIVVETDGDEILMRRLSDESRKRDLETTASIEEHQFMNRAAAMSYGVLTGATVKIVKNKNGLVDNAVEELMSVLR 192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain G from PDB  Type:PROTEIN  Length:191
 aligned with KADA_METMP | Q6LYG0 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_METMP     2 KNKVVVVTGVPGVGGTTVTQKAMDILSEEGLNYKMVNFGSAMFDVANEEGLASDRDQMRRLDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVKTPKGYLPGLPAWVLTELNPDIVIVVETDGDEILMRRLSDESRKRDLETTASIEEHQFMNRAAAMSYGVLTGATVKIVKNKNGLVDNAVEELMSVLR 192
               SCOP domains d3h86g_ G: automated matches                                                                                                                                                                    SCOP domains
               CATH domains 3h86G00 G:2-192 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.eeee...eeee..eeee..hhhhhhhhh..eeeeee.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h86 G   2 KNKVVVVTGVPGVGGTTVTQKAMDILSEEGLNYKMVNFGSAMFDVANEEGLASDRDQMRKLDPETQKRIQKMAGRKIAEMAKESPVAVDTHSTVKTPKGYLPGLPAWVLTELNPDIVIVVETDGDEILMRRLSDESRKRDLETTASIEEHQFMNRAAAMSYGVLTGATVKIVKNKNGLVDNAVEELMSVLR 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: automated matches (25)

Methanococcus maripaludis [TaxId: 39152] (1)

1a	d3h86a_	A:
1b	d3h86b_	B:
1c	d3h86c_	C:
1d	d3h86g_	G:

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 maripaludis. Organism_taxid: 39152. Strain: atcc 43000d. (1)

1a	3h86A00	A:2-192
1b	3h86B00	B:2-192
1c	3h86C00	C:2-192
1d	3h86G00	G:2-192

(no "Pfam Domain" information available for 3H86)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,G (KADA_METMP | Q6LYG0)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3h86)

Biological Units
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	3h86
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1ki9	ADENYLATE KINASE FROM THERMOPHILE METHANOCOCCUS THERMOLITHOTROPHICUS
1kht	ADENYLATE KINASE FROM MESOPHILE METHANOCOCCUS VOLTAE

Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

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Exons (0, 0)

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