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(-) Description

Title :  STRUCTURE OF STREPTOCOCCUS PNEMONIAE PEPTIDOGLYCAN DEACETYLASE (SPPGDA) D 275 N MUTANT.
 
Authors :  D. E. Blair, A. W. Schuttelkopf, J. I. Macrae, D. M. F. Van Aalten
Date :  15 Sep 05  (Deposition) - 20 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Ce-4, Carbohydrate Esterase, Peptidoglycan Deacetylase, Metalloenzyme, D275N Mutant, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Blair, A. W. Schuttelkopf, J. I. Macrae, D. M. F. Van Aalten
Structure And Metal-Dependent Mechanism Of Peptidoglycan Deacetylase, A Streptococcal Virulence Factor.
Proc. Natl. Acad. Sci. Usa V. 102 15429 2005
PubMed-ID: 16221761  |  Reference-DOI: 10.1073/PNAS.0504339102

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN GLCNAC DEACETYLASE
    Atcc: BAA-255
    Chains: A
    EC Number: 3.5.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)PLYSS
    Expression System Plasmid: PGEX-6P-1
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6
    Synonym: SPPGDA-D275N ZN SULPHATE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2SO41Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:276 , HIS A:326 , HIS A:330 , SO4 A:1467BINDING SITE FOR RESIDUE ZN A1465
2AC2SOFTWAREGLU A:144 , GLU A:146 , GLU A:340 , HOH A:2209BINDING SITE FOR RESIDUE ZN A1466
3AC3SOFTWAREASN A:275 , ASP A:276 , HIS A:326 , HIS A:330 , PRO A:366 , TYR A:367 , HIS A:417 , MES A:1464 , ZN A:1465 , HOH A:2210 , HOH A:2211BINDING SITE FOR RESIDUE SO4 A1467
4AC4SOFTWARETYR A:367 , TRP A:385 , ASP A:388 , TRP A:392 , SO4 A:1467BINDING SITE FOR RESIDUE MES A1464

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C1I)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:277 -Pro A:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C1I)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NODBPS51677 NodB homology domain profile.PGDA_STRR6268-442  1A:268-442

(-) Exons   (0, 0)

(no "Exon" information available for 2C1I)

(-) 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:383
 aligned with PGDA_STRR6 | Q8DP63 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:418
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455        
           PGDA_STRR6    46 FEQKIESLKKEKDDQLSEGNQKEHFRQGQAEVIAYYPLQGEKVISSVRELINQDVKDKLESKDNLVFYYTEQEESGLKGVVNRNVTKQIYDLVAFKIEETEKTSLGKVHLTEDGQPFTLDQLFSDASKAKEQLIKELTSFIEDKKIEQDQSEQIVKNFSDQDLSAWNFDYKDSQIILYPSPVVENLEEIALPVSAFFDVIQSSYLLEKDAALYQSYFDKKHQKVVALTFDDGPNPATTPQVLETLAKYDIKATFFVLGKNVSGNEDLVKRIKSEGHVVGNHSWSHPILSQLSLDEAKKQITDTEDVLTKVLGSSSKLMRPPYGAITDDIRNSLDLSFIMWDVDSLDWKSKNEASILTEIQHQVANGSIVLMHDIHSPTVNALPRVIEYLKNQGYTFVTIPEMLNTRLKAHELYYSRDE 463
               SCOP domains d2c1ia2 A:46-267 Peptidoglycan GlcNAc deacetylase                                                                                                                                                                             d2c1ia1 A:268-463 Peptidoglycan GlcNAc deacetylase C-terminal domain                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeee..eehhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeeeeee.-----..eeeeeeeeeeeee......hhhhh..hhhhhhhhhhhhhhhh---------------------hhhhh.eeee..eeee.---------.eeee.hhhhhh.hhhh.hhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhh....eeeehhhhh..hhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhh...eee...ee.hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhh....ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NODB  PDB: A:268-442 UniProt: 268-442                                                                                                                                          --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1i A  46 FEQKIESLKKEKDDQLSEGNQKEHFRQGQAEVIAYYPLQGEKVISSVRELINQDVKDKLESKDNLVFYYTEQEESGLKGVVNRNVTKQIYD-----IEETEKTSLGKVHLTEDGQPFTLDQLFSDASKAKEQLIKELTSF---------------------DLSAWNFDYKDSQIILY---------EIALPVSAFFDVIQSSYLLEKDAALYQSYFDKKHQKVVALTFNDGPNPATTPQVLETLAKYDIKATFFVLGKNVSGNEDLVKRIKSEGHVVGNHSWSHPILSQLSLDEAKKQITDTEDVLTKVLGSSSKLMRPPYGAITDDIRNSLDLSFIMWDVDSLDWKSKNEASILTEIQHQVANGSIVLMHDIHSPTVNALPRVIEYLKNQGYTFVTIPEMLNTRLKAHELYYSRDE 463
                                    55        65        75        85        95       105       115       125       135|     |145       155       165       175       185         -         - |     215       | -       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455        
                                                                                                                    136   142                                        185                   207             223       233
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C1I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C1I)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGDA_STRR6 | Q8DP63)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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  Cis Peptide Bonds
    Gly A:277 - Pro A:278   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PGDA_STRR6 | Q8DP63: 2c1g

(-) Related Entries Specified in the PDB File

2c1g STRUCTURE OF STREPTOCOCCUS PNEUMONIAE PEPTIDOGLYCAN DEACETYLASE (SPPGDA)