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(-) Description

Title :  ADENOSINE KINASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH ADENOSINE IN OCCLUDED LOOP CONFORMATION
 
Authors :  L. Romanello, F. R. Bachega, R. C. Garatt, R. Demarco, J. Brandao-Neto, H. M. Pereira
Date :  29 Dec 11  (Deposition) - 14 Nov 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribokinase, Enzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Romanello, J. F. Bachega, A. Cassago, J. Brandao-Neto, R. Demarco, R. C. Garratt, H. D. Pereira
Adenosine Kinase From Schistosoma Mansoni: Structural Basis For The Differential Incorporation Of Nucleoside Analogues.
Acta Crystallogr. , Sect. D V. 69 126 2013
PubMed-ID: 23275171  |  Reference-DOI: 10.1107/S0907444912044800

(-) Compounds

Molecule 1 - PUTATIVE ADENOSINE KINASE
    Chains: A, B
    EC Number: 2.7.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ADENOSINE KINASE
    Gene: SMP_008360
    Organism Common: BLOOD FLUKE
    Organism Scientific: SCHISTOSOMA MANSONI
    Organism Taxid: 6183

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2CL2Ligand/IonCHLORIDE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:14 , LEU A:16 , ASP A:18 , ILE A:38 , LEU A:40 , GLY A:64 , ALA A:65 , ASN A:68 , VAL A:123 , THR A:136 , LEU A:138 , PHE A:169 , ASN A:298 , ASP A:302 , CL A:402 , HOH A:512BINDING SITE FOR RESIDUE ADN A 401
2AC2SOFTWAREASN A:14 , THR A:66 , ADN A:401BINDING SITE FOR RESIDUE CL A 402
3AC3SOFTWAREASN B:14 , LEU B:16 , ASP B:18 , ILE B:38 , LEU B:40 , GLY B:64 , ALA B:65 , ASN B:68 , VAL B:123 , THR B:136 , LEU B:138 , PHE B:169 , ASN B:298 , GLY B:299 , ASP B:302 , CL B:402 , HOH B:518BINDING SITE FOR RESIDUE ADN B 401
4AC4SOFTWAREASN B:14 , THR B:66 , ADN B:401 , HOH B:502BINDING SITE FOR RESIDUE CL B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:116 -Pro A:117
2Glu B:116 -Pro B:117
3Thr B:297 -Asn B:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VAS)

(-) 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:345
 aligned with G4V7G8_SCHMA | G4V7G8 from UniProtKB/TrEMBL  Length:352

    Alignment length:345
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342     
         G4V7G8_SCHMA     3 DLSEGYVFGMGNPLLDIIVDADDFMYRKYNLKKDNIVLAEEKHMTIYDEIQKKKKLNYIAGGATLNTVKMIQWIIQKPFVCSYVGCIGADIQGKYIKNDCSALDLVTEFQIAEEPLMTGKVAVLVSEKLRSMVTYLGAACDLSLAHIEQPHVWSLVEKAQVYYIAGFVINTCYEGMLKIAKHSLENEKLFCFNLSAPFLSQFNTKEVDEMISYSNIVFGNESEAEAYGEVHGLLEDTVHATARYIADLPFADGKKRKRLVIITRGKNPLLYTDSSDSEIHQFMVEQFKDDQIIDTNGAGDAFAAGFIADYIRGKPMITSLHAAVKAAAYIICRSGFSLGSRDSYS 347
               SCOP domains d3vasa_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..eeeeeee..hhhhhhh.....eeee.hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh..ee..ee......eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh....hhhhhhhhhhhhh..........eeeeee..eeeeeee......eee..............hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vas A   3 DLSEGYVFGMGNPLLDIIVDADDFMYRKYNLKKDNIVLAEEKHMTIYDEIQKKKKLNYIAGGATLNTVKMIQWIIQKPFVCSYVGCIGADIQGKYIKNDCSALDLVTEFQIAEEPLMTGKVAVLVSEKLRSMVTYLGAACDLSLAHIEQPHVWSLVEKAQVYYIAGFVINTCYEGMLKIAKHSLENEKLFCFNLSAPFLSQFNTKEVDEMISYSNIVFGNESEAEAYGEVHGLLEDTVHATARYIADLPFADGKKRKRLVIITRGKNPLLYTDSSDSEIHQFMVEQFKDDQIIDTNGAGDAFAAGFIADYIRGKPMITSLHAAVKAAAYIICRSGFSLGSRDSYS 347
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342     


Chain B from PDB  Type:PROTEIN  Length:343
 aligned with G4V7G8_SCHMA | G4V7G8 from UniProtKB/TrEMBL  Length:352

    Alignment length:345
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342     
         G4V7G8_SCHMA     3 DLSEGYVFGMGNPLLDIIVDADDFMYRKYNLKKDNIVLAEEKHMTIYDEIQKKKKLNYIAGGATLNTVKMIQWIIQKPFVCSYVGCIGADIQGKYIKNDCSALDLVTEFQIAEEPLMTGKVAVLVSEKLRSMVTYLGAACDLSLAHIEQPHVWSLVEKAQVYYIAGFVINTCYEGMLKIAKHSLENEKLFCFNLSAPFLSQFNTKEVDEMISYSNIVFGNESEAEAYGEVHGLLEDTVHATARYIADLPFADGKKRKRLVIITRGKNPLLYTDSSDSEIHQFMVEQFKDDQIIDTNGAGDAFAAGFIADYIRGKPMITSLHAAVKAAAYIICRSGFSLGSRDSYS 347
               SCOP domains d3vasb_ B: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..eeeeeee..hhhhhhh......eee.hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh..eeeeee......eeeeeeee.--...eeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh....hhhhhhhhhhhhh..........eeeeee..eeeeeee......eee.............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vas B   3 DLSEGYVFGMGNPLLDIIVDADDFMYRKYNLKKDNIVLAEEKHMTIYDEIQKKKKLNYIAGGATLNTVKMIQWIIQKPFVCSYVGCIGADIQGKYIKNDCSALDLVTEFQIAEEPLMTGKVAVLVS--LRSMVTYLGAACDLSLAHIEQPHVWSLVEKAQVYYIAGFVINTCYEGMLKIAKHSLENEKLFCFNLSAPFLSQFNTKEVDEMISYSNIVFGNESEAEAYGEVHGLLEDTVHATARYIADLPFADGKKRKRLVIITRGKNPLLYTDSSDSEIHQFMVEQFKDDQIIDTNGAGDAFAAGFIADYIRGKPMITSLHAAVKAAAYIICRSGFSLGSRDSYS 347
                                    12        22        32        42        52        62        72        82        92       102       112       122     | 132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342     
                                                                                                                                                       128  |                                                                                                                                                                                                                        
                                                                                                                                                          131
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (G4V7G8_SCHMA | G4V7G8)
molecular function
    GO:0004001    adenosine kinase activity    Catalysis of the reaction: ATP + adenosine = ADP + AMP.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol 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:0006167    AMP biosynthetic process    The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
    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:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.

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 Related Entries

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

UniProtKB/TrEMBL
        G4V7G8_SCHMA | G4V7G8: 3uq6 3uq9 3vaq 4dc3

(-) Related Entries Specified in the PDB File

3uq6 SCHISTOSOMA ADENOSINE KINASE IN COMPLEX WITH ADENOSINE AND AMP
3uq9 SCHISTOSOMA ADENOSINE KINASE IN COMPLEX WITH TUBERCIDIN
3vaq SCHISTOSOMA ADENOSINE KINASE IN COMPLEX WITH ADENOSINE