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(-) Description

Title :  CRYSTAL STRUCTURE OF RV3168 WITH ATP
 
Authors :  Y. -G. Kim, S. Kim, C. M. T. Nguyen, K. -J. Kim
Date :  13 Jan 11  (Deposition) - 03 Aug 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hypothetical Protein, Putative Aminoglycoside Phosphortransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kim, C. M. T. Nguyen, E. -J. Kim, K. -J. Kim
Crystal Structure Of Mycobacterium Tuberculosis Rv3168: A Putative Aminoglycoside Antibiotics Resistance Enzyme
Proteins V. 79 2983 2011
PubMed-ID: 21905120  |  Reference-DOI: 10.1002/PROT.23119

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 22-378
    Gene: MT3257, RV3168
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CA2Ligand/IonCALCIUM ION
4GOL1Ligand/IonGLYCEROL
5MG2Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:267 , GLU A:269 , ATP A:510 , ACT A:1209BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWAREASN A:254 , ASP A:267 , ATP A:510BINDING SITE FOR RESIDUE MG A 379
3AC3SOFTWAREGLN A:74 , GLY A:375 , GLU A:377 , HOH A:397 , HOH A:421 , HOH A:438BINDING SITE FOR RESIDUE CA A 380
4AC4SOFTWAREMG A:1 , ASP A:249 , GLU A:269BINDING SITE FOR RESIDUE ACT A 1209
5AC5SOFTWAREGLY A:106 , THR A:109 , HOH A:425BINDING SITE FOR RESIDUE CA A 381
6AC6SOFTWAREPHE A:90 , THR A:92 , TYR A:93 , ARG A:94 , GLN A:98 , TRP A:205 , GLU A:269 , HOH A:391 , HOH A:532BINDING SITE FOR RESIDUE GOL A 3545
7AC7SOFTWAREMG A:1 , HOH A:17 , THR A:58 , VAL A:77 , ARG A:79 , PRO A:114 , MET A:133 , ASP A:134 , TYR A:135 , VAL A:136 , VAL A:140 , ASN A:254 , LEU A:256 , LEU A:266 , ASP A:267 , GLU A:269 , MG A:379 , HOH A:449 , HOH A:485 , HOH A:566BINDING SITE FOR RESIDUE ATP A 510

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:144 -Met A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ATT)

(-) 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:352
 aligned with Y3168_MYCTO | P9WI98 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:357
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       
          Y3168_MYCTO    22 TLPAVISRWLSSVLPGGAAPEVTVESGVDSTGMSSETIILTARWQQDGRSIQQKLVARVAPAAEDVPVFPTYRLDHQFEVIRLVGELTDVPVPRVRWIETTGDVLGTPFFLMDYVEGVVPPDVMPYTFGDNWFADAPAERQRQLQDATVAALATLHSIPNAQNTFSFLTQGRTSDTTLHRHFNWVRSWYDFAVEGIGRSPLLERTFEWLQSHWPDDAAAREPVLLWGDARVGNVLYRDFQPVAVLDWEMVALGPRELDVAWMIFAHRVFQELAGLATLPGLPEVMREDDVRATYQALTGVELGDLHWFYVYSGVMWACVFMRTGARRVHFGEIEKPDDVESLFYHAGLMKHLLGEEH 378
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh......eeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeee..hhhhh......hhhhhhhhhhhhhhhh......eeeee.........eeeee...........hhhhh.......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh-----.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhh..eee....hhh.eeee..eeeee......eee.hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3att A  22 TLPAVISRWLSSVLPGGAAPEVTVESGVDSTGMSSETIILTARWQQDGRSIQQKLVARVAPAAEDVPVFPTYRLDHQFEVIRLVGELTDVPVPRVRWIETTGDVLGTPFFLMDYVEGVVPPDVMPYTFGDNWFADAPAERQRQLQDATVAALATLHSIPNAQNTFSFLT-----DTTLHRHFNWVRSWYDFAVEGIGRSPLLERTFEWLQSHWPDDAAAREPVLLWGDARVGNVLYRDFQPVAVLDWEMVALGPRELDVAWMIFAHRVFQELAGLATLPGLPEVMREDDVRATYQALTGVELGDLHWFYVYSGVMWACVFMRTGARRVHFGEIEKPDDVESLFYHAGLMKHLLGEEH 378
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        |-    |  201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       
                                                                                                                                                                                                  190   196                                                                                                                                                                                      


Chain A from PDB  Type:PROTEIN  Length:352
 aligned with Y3168_MYCTU | P9WI99 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:357
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       
          Y3168_MYCTU    22 TLPAVISRWLSSVLPGGAAPEVTVESGVDSTGMSSETIILTARWQQDGRSIQQKLVARVAPAAEDVPVFPTYRLDHQFEVIRLVGELTDVPVPRVRWIETTGDVLGTPFFLMDYVEGVVPPDVMPYTFGDNWFADAPAERQRQLQDATVAALATLHSIPNAQNTFSFLTQGRTSDTTLHRHFNWVRSWYDFAVEGIGRSPLLERTFEWLQSHWPDDAAAREPVLLWGDARVGNVLYRDFQPVAVLDWEMVALGPRELDVAWMIFAHRVFQELAGLATLPGLPEVMREDDVRATYQALTGVELGDLHWFYVYSGVMWACVFMRTGARRVHFGEIEKPDDVESLFYHAGLMKHLLGEEH 378
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh......eeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeee..hhhhh......hhhhhhhhhhhhhhhh......eeeee.........eeeee...........hhhhh.......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh-----.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhh..eee....hhh.eeee..eeeee......eee.hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3att A  22 TLPAVISRWLSSVLPGGAAPEVTVESGVDSTGMSSETIILTARWQQDGRSIQQKLVARVAPAAEDVPVFPTYRLDHQFEVIRLVGELTDVPVPRVRWIETTGDVLGTPFFLMDYVEGVVPPDVMPYTFGDNWFADAPAERQRQLQDATVAALATLHSIPNAQNTFSFLT-----DTTLHRHFNWVRSWYDFAVEGIGRSPLLERTFEWLQSHWPDDAAAREPVLLWGDARVGNVLYRDFQPVAVLDWEMVALGPRELDVAWMIFAHRVFQELAGLATLPGLPEVMREDDVRATYQALTGVELGDLHWFYVYSGVMWACVFMRTGARRVHFGEIEKPDDVESLFYHAGLMKHLLGEEH 378
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        |-    |  201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       
                                                                                                                                                                                                  190   196
   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 3ATT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Y3168_MYCTU | P9WI99)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Chain A   (Y3168_MYCTO | P9WI98)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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(-) Related Entries Specified in the PDB File

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