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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ADENYLATE KINASE COMPLEXED WITH TWO MOLECULES OF ADP AND MG
 
Authors :  M. Bellinzoni, A. Haouz, M. Grana, H. Munier-Lehmann, P. M. Alzari
Date :  25 Jan 06  (Deposition) - 10 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Adenylate Kinase, Phosphoryl Transfer, Associative Mechanism, Atp-Binding, Kinase, Nucleotide Biosynthesis, Nucleotide-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bellinzoni, A. Haouz, M. Grana, H. Munier-Lehmann, W. Shepard, P. M. Alzari
The Crystal Structure Of Mycobacterium Tuberculosis Adenylate Kinase In Complex With Two Molecules Of Adp And Mg2+ Supports An Associative Mechanism For Phosphoryl Transfer.
Protein Sci. V. 15 1489 2006
PubMed-ID: 16672241  |  Reference-DOI: 10.1110/PS.062163406

(-) Compounds

Molecule 1 - ADENYLATE KINASE
    Chains: A
    EC Number: 2.7.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-28A
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: ATP-AMP TRANSPHOSPHORYLASE, AK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREADP A:201 , ADP A:202 , HOH A:2062 , HOH A:2126BINDING SITE FOR RESIDUE MG A 200
2AC2SOFTWARELYS A:13 , THR A:31 , GLY A:32 , ARG A:36 , LEU A:53 , ASP A:57 , LEU A:58 , VAL A:59 , THR A:64 , GLY A:85 , TYR A:86 , ARG A:88 , GLN A:92 , ARG A:127 , ARG A:129 , ARG A:140 , MG A:200 , ADP A:202 , HOH A:2062 , HOH A:2091 , HOH A:2125 , HOH A:2126 , HOH A:2127 , HOH A:2128BINDING SITE FOR RESIDUE ADP A 201
3AC3SOFTWAREGLY A:10 , ALA A:11 , GLY A:12 , LYS A:13 , GLY A:14 , THR A:15 , ARG A:123 , ARG A:127 , GLY A:166 , THR A:167 , MET A:168 , MG A:200 , ADP A:201 , HOH A:2014 , HOH A:2062 , HOH A:2083 , HOH A:2129 , HOH A:2130 , HOH A:2131 , HOH A:2132 , HOH A:2133 , HOH A:2134BINDING SITE FOR RESIDUE ADP A 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:86 -Pro A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD_MYCTO81-92  1A:81-92
KAD_MYCTU81-92  1A:81-92

(-) Exons   (0, 0)

(no "Exon" information available for 2CDN)

(-) 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:186
 aligned with KAD_MYCTO | P9WKF4 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:186
                                 1                                                                                                                                                                                    
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      
            KAD_MYCTO     - -----MRVLLLGPPGAGKGTQAVKLAEKLGIPQISTGELFRRNIEEGTKLGVEAKRYLDAGDLVPSDLTNELVDDRLNNPDAANGFILDGYPRSVEQAKALHEMLERRGTDIDAVLEFRVSEEVLLERLKGRGRADDTDDVILNRMKVYRDETAPLLEYYRDQLKTVDAVGTMDEVFARALRALGK 181
               SCOP domains d2cdna_ A: Adenylate kinase                                                                                                                                                                SCOP domains
               CATH domains 2cdnA00 A:-4-181 P-loop containing nucleotide triphosphate hydrolases                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhh...eeeee...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------ADENYLATE_KI----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cdn A  -4 PRGSHMRVLLLGPPGAGKGTQAVKLAEKLGIPQISTGELFRRNIEEGTKLGVEAKRYLDAGDLVPSDLTNELVDDRLNNPDAANGFILDGYPRSVEQAKALHEMLERRGTDIDAVLEFRVSEEVLLERLKGRGRADDTDDVILNRMKVYRDETAPLLEYYRDQLKTVDAVGTMDEVFARALRALGK 181
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      


Chain A from PDB  Type:PROTEIN  Length:186
 aligned with KAD_MYCTU | P9WKF5 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:186
                                 1                                                                                                                                                                                    
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      
            KAD_MYCTU     - -----MRVLLLGPPGAGKGTQAVKLAEKLGIPQISTGELFRRNIEEGTKLGVEAKRYLDAGDLVPSDLTNELVDDRLNNPDAANGFILDGYPRSVEQAKALHEMLERRGTDIDAVLEFRVSEEVLLERLKGRGRADDTDDVILNRMKVYRDETAPLLEYYRDQLKTVDAVGTMDEVFARALRALGK 181
               SCOP domains d2cdna_ A: Adenylate kinase                                                                                                                                                                SCOP domains
               CATH domains 2cdnA00 A:-4-181 P-loop containing nucleotide triphosphate hydrolases                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhh...eeeee...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------ADENYLATE_KI----------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cdn A  -4 PRGSHMRVLLLGPPGAGKGTQAVKLAEKLGIPQISTGELFRRNIEEGTKLGVEAKRYLDAGDLVPSDLTNELVDDRLNNPDAANGFILDGYPRSVEQAKALHEMLERRGTDIDAVLEFRVSEEVLLERLKGRGRADDTDDVILNRMKVYRDETAPLLEYYRDQLKTVDAVGTMDEVFARALRALGK 181
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KAD_MYCTU | P9WKF5)
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:0004550    nucleoside diphosphate kinase activity    Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
    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: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:0009132    nucleoside diphosphate metabolic process    The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar.
    GO:0006165    nucleoside diphosphate phosphorylation    The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
    GO:0009123    nucleoside monophosphate metabolic process    The chemical reactions and pathways involving a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar.
    GO:0009141    nucleoside triphosphate metabolic process    The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    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.
    GO:0006144    purine nucleobase metabolic process    The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A   (KAD_MYCTO | P9WKF4)
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: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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  2cdn
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KAD_MYCTO | P9WKF4: 1p4s
        KAD_MYCTU | P9WKF5: 1p4s

(-) Related Entries Specified in the PDB File

1p4s SOLUTION STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ADENYLATE KINASE