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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOGLYCOSIDE-2''-PHOSPHOTRANSFERASE TYPE IVA IN COMPLEX WITH GUANOSINE
 
Authors :  K. Shi, A. M. Berghuis
Date :  20 Feb 12  (Deposition) - 07 Mar 12  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Aminoglycoside Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Shi, A. M. Berghuis
Structural Basis For Dual Nucleotide Selectivity Of Aminoglycoside 2''-Phosphotransferase Iva Provides Insight On Determinants Of Nucleotide Specificity Of Aminoglycoside Kinases.
J. Biol. Chem. V. 287 13094 2012
PubMed-ID: 22371504  |  Reference-DOI: 10.1074/JBC.M112.349670

(-) Compounds

Molecule 1 - APH(2'')-ID
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: APH(2'')-ID
    Organism Scientific: ENTEROCOCCUS CASSELIFLAVUS
    Organism Taxid: 37734

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GMP2Ligand/IonGUANOSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GMP1Ligand/IonGUANOSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GMP1Ligand/IonGUANOSINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GMP2Ligand/IonGUANOSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:28 , GLY A:29 , ALA A:36 , ILE A:44 , LYS A:46 , ILE A:98 , GLY A:100 , ILE A:216 , ASP A:217 , HOH A:501 , HOH A:502 , HOH A:529 , HOH A:530 , HOH A:569BINDING SITE FOR RESIDUE GMP A 401
2AC2SOFTWARESER B:28 , GLY B:29 , GLU B:30 , ALA B:36 , ILE B:44 , LYS B:46 , LYS B:97 , ILE B:98 , GLY B:100 , LEU B:204 , ILE B:216 , ASP B:217 , HOH B:501 , HOH B:502 , HOH B:534 , HOH B:571 , HOH B:612BINDING SITE FOR RESIDUE GMP B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DT9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DT9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DT9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DT9)

(-) Exons   (0, 0)

(no "Exon" information available for 4DT9)

(-) 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:296
 aligned with O68183_ENTCA | O68183 from UniProtKB/TrEMBL  Length:301

    Alignment length:296
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      
         O68183_ENTCA     1 MRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIR 296
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.........eeee...eeeee.....eeeee.hhhhhhhhhhhhhhhhhhh.........eeee...........eee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eee....hhh.eeee....eeeee......eee..hhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dt9 A   1 MRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIR 296
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with O68183_ENTCA | O68183 from UniProtKB/TrEMBL  Length:301

    Alignment length:298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        
         O68183_ENTCA     1 MRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSI 298
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.......eeeeee...eeeeee...eeeeee.hhhhhhhhhhhhhhhhhhh.........eeee...........eeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eee....hhh.eeee....eeeee......eee..hhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dt9 B   1 MRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSI 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   Legend:   → Mismatch (orange background)
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  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 4DT9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DT9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DT9)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O68183_ENTCA | O68183)
molecular function
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        O68183_ENTCA | O68183: 3n4t 3n4u 3n4v 3sg8 3sg9 3sgc 4dbx 4de4 4dfb 4dfu 4dt8 4dta 4dtb 4n57 5c4k 5c4l

(-) Related Entries Specified in the PDB File

4dt8 4dta 4dtb