2AK3 - JenaLib

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Title :   THE THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN MITOCHONDRIAL MATRIX ADENYLATE KINASE AND ITS SUBSTRATE AMP AT 1.85 ANGSTROMS RESOLUTION

Authors :   K. Diederichs, G. E. Schulz

Date :   07 Mar 95 (Deposition) - 08 May 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

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

Reference :   K. Diederichs, G. E. Schulz
The Refined Structure Of The Complex Between Adenylate Kinase From Beef Heart Mitochondrial Matrix And Its Substrate Amp At 1. 85 A Resolution.
J. Mol. Biol. V. 217 541 1991
PubMed-ID: 1994037 | Reference-DOI: 10.1016/0022-2836(91)90756-V
(for further references see the PDB file header)

Molecule 1 - ADENYLATE KINASE ISOENZYME-3
	Chains	:	A, B
	EC Number	:	2.7.4.10
	Engineered	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

		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	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:13 , GLY A:15 , SER A:16 , GLY A:17 , LYS A:18 , GLY A:19 , HOH A:324	BINDING SITE FOR RESIDUE SO4 A 227
2	AC2	SOFTWARE	GLY B:15 , SER B:16 , GLY B:17 , LYS B:18 , GLY B:19 , HOH B:332 , HOH B:392 , HOH B:395	BINDING SITE FOR RESIDUE SO4 B 227
3	AC3	SOFTWARE	SER A:36 , LEU A:40 , ARG A:41 , ILE A:58 , LYS A:62 , LEU A:63 , ILE A:64 , MET A:69 , GLY A:89 , ARG A:92 , GLN A:96 , HOH A:338 , HOH A:374 , HOH A:409	BINDING SITE FOR RESIDUE AMP A 226
4	AC4	SOFTWARE	SER B:36 , GLY B:37 , LEU B:40 , ARG B:41 , ILE B:58 , LYS B:62 , LEU B:63 , ILE B:64 , MET B:69 , GLY B:89 , ARG B:92 , GLN B:96 , HOH B:293 , HOH B:328 , HOH B:330	BINDING SITE FOR RESIDUE AMP B 226

(no "SS Bond" information available for 2AK3)

Asymmetric Unit

No.	Residues
1	Phe A:90	-	Pro A:91
2	Phe B:90	-	Pro B:91

(no "SAP(SNP)/Variant" information available for 2AK3)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD3_BOVIN	87-98	2	A:85-96 B:85-96

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD3_BOVIN	87-98	1	A:85-96 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLATE_KINASE	PS00113	Adenylate kinase signature.	KAD3_BOVIN	87-98	1	- B:85-96

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000022789	1	ENSBTAE00000353662	chr8:42002117-42002405	289	KAD3_BOVIN	1-51	51	2	A:0-49 B:0-49	50 50
1.2	ENSBTAT00000022789	2	ENSBTAE00000186230	chr8:42012911-42013030	120	KAD3_BOVIN	51-91	41	2	A:49-89 B:49-89	41 41
1.3	ENSBTAT00000022789	3	ENSBTAE00000186236	chr8:42014003-42014175	173	KAD3_BOVIN	91-148	58	2	A:89-146 B:89-146	58 58
1.4	ENSBTAT00000022789	4	ENSBTAE00000186239	chr8:42015061-42015179	119	KAD3_BOVIN	149-188	40	2	A:147-186 B:147-186	40 40
1.5	ENSBTAT00000022789	5	ENSBTAE00000186241	chr8:42021169-42024098	2930	KAD3_BOVIN	188-227	40	2	A:186-225 B:186-220	40 35

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
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Chain A from PDB  Type:PROTEIN  Length:226
 aligned with KAD3_BOVIN | P08760 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      
           KAD3_BOVIN     2 GASARLLRAAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLAKTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGEPLVQREDDRPETVVKRLKAYEAQTEPVLEYYRKKGVLETFSGTETNKIWPHVYAFLQTKLPQRSQETSVTP 227
               SCOP domains d2ak3a1 A:0-124,A:162-225 Adenylate kinase                                                                                   d2ak3a2 A:125-161                    d2ak3a1 A:0-124,A:162-225 Adenylate kinase                       SCOP domains
               CATH domains 2ak3A00 A:0-225 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ......eeeeee.....hhhhhhhhhhhhh..----hhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeee....hhhhhhhhh......eeeeee.hhhhhhhhh.eeeee....eeeee........eee....eeee.....hhhhhhhhhhhhhhhhh.hhhhhhhh.eeeeeee.....hhhhhhhhhh.............. Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------eeeee--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------ADENYLATE_KI--------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:0-49 UniProt: 1-51 [INCOMPLETE]  ---------------------------------------Exon 1.3  PDB: A:89-146 UniProt: 91-148                   Exon 1.4  PDB: A:147-186                --------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.2  PDB: A:49-89 UniProt: 51-91    ------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:186-225                 Transcript 1 (2)
                 2ak3 A   0 GASARLLRAAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLAKTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGEPLVQREDDRPETVVKRLKAYEAQTEPVLEYYRKKGVLETFSGTETNKIWPHVYAFLQTKLPQRSQETSVTP 225
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with KAD3_BOVIN | P08760 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
           KAD3_BOVIN     2 GASARLLRAAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLAKTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGEPLVQREDDRPETVVKRLKAYEAQTEPVLEYYRKKGVLETFSGTETNKIWPHVYAFLQTKLPQRSQE 222
               SCOP domains d2ak3b1 B:0-124,B:162-220 Adenylate kinase                                                                                   d2ak3b2 B:125-161                    d2ak3b1 B:0-124,B:162-220 Adenylate kinase                  SCOP domains
               CATH domains 2ak3B00 B:0-220 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ......eeeeee.....hhhhhhhhhhhhh..----hhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeee....hhhhhhhhh......eeeeee.hhhhhhhhh.eeeee....eeeee........eee....eeee.....hhhhhhhhhhhhhhhhh.hhhhhhhh.eeeeeee.....hhhhhhhhhh......... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------eeeee---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------ADENYLATE_KI---------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:0-49 UniProt: 1-51 [INCOMPLETE]  ---------------------------------------Exon 1.3  PDB: B:89-146 UniProt: 91-148                   Exon 1.4  PDB: B:147-186                ---------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.2  PDB: B:49-89 UniProt: 51-91    ------------------------------------------------------------------------------------------------Exon 1.5  PDB: B:186-220            Transcript 1 (2)
                 2ak3 B   0 GASARLLRAAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLAKTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGEPLVQREDDRPETVVKRLKAYEAQTEPVLEYYRKKGVLETFSGTETNKIWPHVYAFLQTKLPQRSQE 220
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219

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(

)

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)

Cattle (Bos taurus) (17)

1a	2ak3B00	B:0-220
1b	2ak3A00	A:0-225

(no "Pfam Domain" information available for 2AK3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KAD3_BOVIN | P08760)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	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:0046899	nucleoside triphosphate adenylate kinase activity	Catalysis of the reaction: nucleoside triphosphate + AMP = nucleoside diphosphate + ADP.
	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:0006172	ADP biosynthetic process	The chemical reactions and pathways resulting in the formation of ADP, adenosine 5'-diphosphate.
	GO:0046033	AMP metabolic process	The chemical reactions and pathways involving AMP, adenosine monophosphate.
	GO:0046039	GTP metabolic process	The chemical reactions and pathways involving GTP, guanosine triphosphate.
	GO:0046041	ITP metabolic process	The chemical reactions and pathways involving ITP, inosine triphosphate.
	GO:0046051	UTP metabolic process	The chemical reactions and pathways involving UTP, uridine (5'-)triphosphate.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	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:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (2, 4)

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