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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOSPHORYL TRANSFER TRANSITION STATE MIMIC IN THE ADENYLATE KINASE: ADP/ALF4/AMP IN THE ACTIVE SITE
 
Authors :  Y. -J. Cho, D. Kern
Date :  06 Jul 11  (Deposition) - 10 Oct 12  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Phosphoryl Transfer Analogue, Alf4, Transferase (Phosphotransferase), Phosphoryl Transfer, Nucleotide-Binding, Phosphoryl Transfer Of Nucleotides, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Kerns, R. V. Agafonov, Y. J. Cho, F. Pontiggia, R. Otten, D. V. Pachov, S. Kutter, L. A. Phung, P. N. Murphy, V. Thai, T. Alber, M. F. Hagan, D. Kern
The Energy Landscape Of Adenylate Kinase During Catalysis.
Nat. Struct. Mol. Biol. V. 22 124 2015
PubMed-ID: 25580578  |  Reference-DOI: 10.1038/NSMB.2941

(-) Compounds

Molecule 1 - ADENYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ADK, AQUIFEX, AQ_078
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: AK, ATP-AMP TRANSPHOSPHORYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF2Ligand/IonTETRAFLUOROALUMINATE ION
3AMP2Ligand/IonADENOSINE MONOPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF1Ligand/IonTETRAFLUOROALUMINATE ION
3AMP1Ligand/IonADENOSINE MONOPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF1Ligand/IonTETRAFLUOROALUMINATE ION
3AMP1Ligand/IonADENOSINE MONOPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , ALA A:11 , GLY A:12 , LYS A:13 , GLY A:14 , THR A:15 , ARG A:120 , ARG A:124 , VAL A:133 , TYR A:134 , HIS A:135 , TYR A:138 , LYS A:189 , PRO A:190 , VAL A:191 , MG A:209 , ALF A:210 , HOH A:232 , HOH A:255 , HOH A:314 , ARG B:55BINDING SITE FOR RESIDUE ADP A 207
2AC2SOFTWARETHR A:31 , GLY A:32 , LEU A:35 , ARG A:36 , MET A:53 , GLU A:57 , VAL A:59 , ILE A:64 , GLY A:82 , ARG A:85 , GLN A:89 , ARG A:150 , ARG A:161 , ALF A:210 , HOH A:218 , HOH A:238 , HOH A:259 , HOH A:322 , HOH A:332BINDING SITE FOR RESIDUE AMP A 208
3AC3SOFTWAREADP A:207 , ALF A:210 , HOH A:314 , HOH A:332BINDING SITE FOR RESIDUE MG A 209
4AC4SOFTWAREPRO A:9 , LYS A:13 , ARG A:85 , ARG A:124 , ARG A:150 , ARG A:161 , ADP A:207 , AMP A:208 , MG A:209 , HOH A:232 , HOH A:238 , HOH A:314 , HOH A:332 , HOH A:712BINDING SITE FOR RESIDUE ALF A 210
5AC5SOFTWAREGLY B:10 , ALA B:11 , GLY B:12 , LYS B:13 , GLY B:14 , THR B:15 , ARG B:120 , ARG B:124 , TYR B:134 , HIS B:135 , TYR B:138 , LYS B:189 , PRO B:190 , VAL B:191 , MG B:209 , ALF B:210 , HOH B:216 , HOH B:245 , HOH B:246 , HOH B:475 , HOH B:635BINDING SITE FOR RESIDUE ADP B 207
6AC6SOFTWARETHR B:31 , GLY B:32 , LEU B:35 , ARG B:36 , MET B:53 , GLU B:57 , LEU B:58 , VAL B:59 , ILE B:64 , GLY B:82 , ARG B:85 , GLN B:89 , ARG B:150 , ARG B:161 , ALF B:210 , HOH B:215 , HOH B:219 , HOH B:224 , HOH B:310 , HOH B:348BINDING SITE FOR RESIDUE AMP B 208
7AC7SOFTWAREADP B:207 , ALF B:210 , HOH B:216 , HOH B:348 , HOH B:369BINDING SITE FOR RESIDUE MG B 209
8AC8SOFTWAREPRO B:9 , LYS B:13 , ARG B:124 , ARG B:150 , ARG B:161 , ADP B:207 , AMP B:208 , MG B:209 , HOH B:216 , HOH B:310 , HOH B:348 , HOH B:389 , HOH B:635BINDING SITE FOR RESIDUE ALF B 210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SR0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:83 -Pro A:84
2Phe B:83 -Pro B:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SR0)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD_AQUAE78-89
 		  2A:78-89
B:78-89
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD_AQUAE78-89
 		  1A:78-89
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD_AQUAE78-89
 		  1-
B:78-89

(-) Exons   (0, 0)

(no "Exon" information available for 3SR0)

(-) Sequences/Alignments

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:203
 aligned with KAD_AQUAE | O66490 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   
            KAD_AQUAE     1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVIG 203
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhheee......eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------ADENYLATE_KI------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sr0 A   1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVIG 203
                                    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:203
 aligned with KAD_AQUAE | O66490 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   
            KAD_AQUAE     1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVIG 203
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhheee......eee..............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.eeeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------ADENYLATE_KI------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sr0 B   1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVIG 203
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3SR0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SR0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SR0)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  3sr0
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  2.7.4.3
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 Related Entries

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UniProtKB/Swiss-Prot
        KAD_AQUAE | O66490: 2rgx 2rh5 4cf7 4ike 4jky 4jl5 4jl6 4jl8 4jla 4jlb 4jld 4jlo 4jlp

(-) Related Entries Specified in the PDB File

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