2RH5 - JenaLib

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Title :   STRUCTURE OF APO ADENYLATE KINASE FROM AQUIFEX AEOLICUS

Authors :   V. Thai, M. Wolf-Watz, T Fenn, E. Pozharski, M. A. Wilson, G. A. Petsko, D. Kern

Date :   05 Oct 07 (Deposition) - 18 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.48

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

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

Reference :   K. A. Henzler-Wildman, V. Thai, M. Lei, M. Ott, M. Wolf-Watz, T. Fenn, E. Pozharski, M. A. Wilson, G. A. Petsko, M. Karplus, C. G. Hubner, D. Kern
Intrinsic Motions Along An Enzymatic Reaction Trajectory.
Nature V. 450 838 2007
PubMed-ID: 18026086 | Reference-DOI: 10.1038/NATURE06410
(for further references see the PDB file header)

Molecule 1 - ADENYLATE KINASE
	Chains	:	A, C, B
	EC Number	:	2.7.4.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ADK
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	ATP-AMP TRANSPHOSPHORYLASE

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2RH5)

(no "Site" information available for 2RH5)

(no "SS Bond" information available for 2RH5)

Asymmetric Unit

No.	Residues
1	Phe A:83	-	Pro A:84
2	Phe C:83	-	Pro C:84
3	Phe B:83	-	Pro B:84

(no "SAP(SNP)/Variant" information available for 2RH5)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD_AQUAE	78-89	3	A:78-89 B:78-89 C:78-89

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD_AQUAE	78-89	1	A:78-89 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD_AQUAE	78-89	1	- - C:78-89

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD_AQUAE	78-89	1	- B:78-89 -

(no "Exon" information available for 2RH5)

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:202
 aligned with KAD_AQUAE | O66490 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
            KAD_AQUAE     1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVI 202
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rh5A00 A:1-202 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhheee......eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------ADENYLATE_KI----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rh5 A   1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVI 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with KAD_AQUAE | O66490 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
            KAD_AQUAE     1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVI 202
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rh5B00 B:1-202 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhheee......eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------ADENYLATE_KI----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rh5 B   1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVI 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain C from PDB  Type:PROTEIN  Length:202
 aligned with KAD_AQUAE | O66490 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
            KAD_AQUAE     1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVI 202
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rh5C00 C:1-202 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                       CATH domains
           Pfam domains (1) ----ADK-2rh5C01 C:5-181                                                                                                                                                              --------------------- Pfam domains (1)
           Pfam domains (2) ----ADK-2rh5C02 C:5-181                                                                                                                                                              --------------------- Pfam domains (2)
           Pfam domains (3) ----ADK-2rh5C03 C:5-181                                                                                                                                                              --------------------- Pfam domains (3)
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhh......eeeeee.hhhhhhhhhh.eee......eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------ADENYLATE_KI----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rh5 C   1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVI 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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 2RH5)

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)

Aquifex aeolicus. Organism_taxid: 63363. (7)

1a	2rh5A00	A:1-202
1b	2rh5B00	B:1-202
1c	2rh5C00	C:1-202

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: ADK (22)

Aquifex aeolicus (2)

1a	ADK-2rh5C01	C:5-181
1b	ADK-2rh5C02	C:5-181
1c	ADK-2rh5C03	C:5-181

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (KAD_AQUAE | O66490)

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: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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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Phe A:83 - Pro A:84	[ RasMol ]
		Phe B:83 - Pro B:84	[ RasMol ]
		Phe C:83 - Pro C:84	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
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