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(-) Description

Title :  3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS PNEUMONIAE AT 1.6 A RESOLUTION
 
Authors :  I. Perez-Dorado, R. Sanles, J. A. Hermoso, A. Gonzalez, A. Garcia, P. Ga J. L. Garcia, M. Menendez
Date :  21 Oct 09  (Deposition) - 21 Apr 10  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycosidase, Choline-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Perez-Dorado, A. Gonzalez, M. Morales, R. Sanles, W. Striker, W. Vollmer, S. Mobashery, J. L. Garcia, A. Garcia, M. Martinez-Ripoll P. Garcia, J. A. Hermoso
Insights Into Pneumococcal Fratricide From The Crystal Structures Of The Modular Killing Factor Lytc.
Nat. Struct. Mol. Biol. V. 17 576 2010
PubMed-ID: 20400948  |  Reference-DOI: 10.1038/NSMB.1817
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1,4-BETA-N-ACETYLMURAMIDASE
    Chains: A
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLCC14
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6
    Synonym: LYTC AUTOLYSIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1CHT7Ligand/IonCHOLINE ION
2CL2Ligand/IonCHLORIDE ION
3GOL7Ligand/IonGLYCEROL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:72 , ARG A:76 , TYR A:77 , SER A:78 , GLU A:81 , ARG A:408 , GLN A:412BINDING SITE FOR RESIDUE GOL A 601
02AC2SOFTWARETRP A:135 , TYR A:137 , GLU A:260 , HOH A:2331 , HOH A:2558BINDING SITE FOR RESIDUE GOL A 602
03AC3SOFTWAREASN A:127 , TRP A:129 , GLN A:157 , HOH A:2560BINDING SITE FOR RESIDUE GOL A 603
04AC4SOFTWARETRP A:122 , GLN A:144 , TYR A:147 , CHT A:705BINDING SITE FOR RESIDUE GOL A 604
05AC5SOFTWAREGLN A:142 , TRP A:143 , ASP A:163 , ALA A:165 , TYR A:166 , HOH A:2181 , HOH A:2561BINDING SITE FOR RESIDUE GOL A 605
06AC6SOFTWAREARG A:253 , GLU A:266 , ASP A:294 , HOH A:2562 , HOH A:2563 , HOH A:2564BINDING SITE FOR RESIDUE GOL A 606
07AC7SOFTWARETYR A:302 , TYR A:369 , VAL A:370BINDING SITE FOR RESIDUE GOL A 607
08AC8SOFTWARETRP A:42 , TYR A:65 , PHE A:69 , TYR A:77 , GLY A:91 , TYR A:93BINDING SITE FOR RESIDUE CHT A 701
09AC9SOFTWARETRP A:59 , TRP A:68 , TYR A:86 , MET A:94 , ASP A:114 , HOH A:2071BINDING SITE FOR RESIDUE CHT A 702
10BC1SOFTWARETRP A:82 , GLY A:84 , TYR A:105 , PHE A:109 , TYR A:117 , TRP A:135BINDING SITE FOR RESIDUE CHT A 703
11BC2SOFTWARETRP A:99 , TRP A:108 , TYR A:130 , MET A:138 , GLN A:152BINDING SITE FOR RESIDUE CHT A 704
12BC3SOFTWARETRP A:122 , TRP A:129 , ASP A:175 , GOL A:604BINDING SITE FOR RESIDUE CHT A 705
13BC4SOFTWARETRP A:143 , GLY A:145 , TYR A:166 , PHE A:170 , TYR A:178 , TRP A:196BINDING SITE FOR RESIDUE CHT A 706
14BC5SOFTWARETYR A:191 , MET A:199 , ARG A:201 , SER A:213BINDING SITE FOR RESIDUE CHT A 707
15BC6SOFTWAREASN A:85 , ALA A:116 , TYR A:117 , HIS A:119BINDING SITE FOR RESIDUE CL A 801
16BC7SOFTWAREARG A:408 , SER A:409 , HOH A:2483BINDING SITE FOR RESIDUE CL A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WW5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WW5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WW5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WW5)

(-) Exons   (0, 0)

(no "Exon" information available for 2WW5)

(-) 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:431
 aligned with Q8DP07_STRR6 | Q8DP07 from UniProtKB/TrEMBL  Length:501

    Alignment length:431
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500 
         Q8DP07_STRR6    71 AAAYWDGDYYVKDDGSKAQSEWIFDNYYKAWFYINSDGRYSQNEWHGNYYLKSGGYMAQNEWIYDSNYKSWFYLKSDGAYAHQEWQLIGNKWYYFKKWGYMAKSQWQGSYFLNGQGAMIQNEWLYDPAYSAYFYLKSDGTYANQEWQKVGGKWYYFKKWGYMARNEWQGNYYLTGSGAMATDEVIMDGARYIFAASGELKEKKDLNVGWVHRDGKRYFFNNREEQVGTEHAKKIIDISEHNGRINDWKKVIDENKVDGVIVRLGYSGKEDKELAHNIKELNRLGIPYGVYLYTYAENETDAENDAKQTIELIKKYNMNLSYPIYYDVENWEYVNKSKRAPSDTDTWVKIINKYMDTMKQAGYQNVYVYSYRSLLQTRLKHPDILKHVNWVAAYTNALEWENPYYSGEKGWQYTSSEYMKGIQGRVDVSVWY 501
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2ww5A0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2ww5A0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2ww5A0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2ww5A0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...eee..eee.........eeeee....eeeee.........eee..eeehhhhh....eeeee....eeeee.........eeeee..eeeeehhhhh....eee..eee.........eeee......eeee.........eeeee..eeeeehhhhh....eee..eee.........eeee..eeeee.....eeeeee...eeeee..eeeee.....ee.....eeeeeehhhhh...hhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhh.......eeee...............hhhhhhhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhh.eeeee................eeeeeeeee........eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ww5 A  38 AAAYWDGDYYVKDDGSKAQSEWIFDNYYKAWFYINSDGRYSQNEWHGNYYLKSGGYMAQNEWIYDSNYKSWFYLKSDGAYAHQEWQLIGNKWYYFKKWGYMAKSQWQGSYFLNGQGAMIQNEWLYDPAYSAYFYLKSDGTYANQEWQKVGGKWYYFKKWGYMARNEWQGNYYLTGSGAMATDEVIMDGARYIFAASGELKEKKDLNVGWVHRDGKRYFFNNREEQVGTEHAKKIIDISEHNGRINDWKKVIDENEVDGVIVRLGYSGKEDKELAHNIKELNRLGIPYGVYLYTYAENETDAENDAKQTIELIKKYNMNLSYPIYYDVENWEYVNKSKRAPSDTDTWVKIINKYMDTMKQAGYQNVYVYSYRSLLQTRLKHPDILKHVNWVAAYTNALEWENPYYSGEKGWQYTSSEYMKGIQGRVDVSVWY 468
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467 


Chain A from PDB  Type:PROTEIN  Length:431
 aligned with Q9Z4J8_STREE | Q9Z4J8 from UniProtKB/TrEMBL  Length:501

    Alignment length:431
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500 
         Q9Z4J8_STREE    71 AAAYWDGDYYVKDDGSKAQSEWIFDNYYKAWFYINSDGRYSQNEWHGNYYLKSGGYMAQNEWIYDSNYKSWFYLKSDGAYAHQEWQLIGNKWYYFKKWGYMAKSQWQGSYFLNGQGAMIQNEWLYDPAYSAYFYLKSDGTYANQEWQKVGGKWYYFKKWGYMARNEWQGNYYLTGSGAMATDEVIMDGARYIFAASGELKEKKDLNVGWVHRDGKRYFFNNREEQVGTEHAKKIIDISEHNGRINDWKKVIDENEVDGVIVRLGYSGKEDKELAHNIKELNRLGIPYGVYLYTYAENETDAENDAKQTIELIKKYNMNLSYPIYYDVENWEYVNKSKRAPSDTDTWVKIINKYMDTMKQAGYQNVYVYSYRSLLQTRLKHPDILKHVNWVAAYTNALEWENPYYSGEKGWQYTSSEYMKGIQGRVDVSVWY 501
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2ww5A0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2ww5A0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2ww5A0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2ww5A0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...eee..eee.........eeeee....eeeee.........eee..eeehhhhh....eeeee....eeeee.........eeeee..eeeeehhhhh....eee..eee.........eeee......eeee.........eeeee..eeeeehhhhh....eee..eee.........eeee..eeeee.....eeeeee...eeeee..eeeee.....ee.....eeeeeehhhhh...hhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhh.......eeee...............hhhhhhhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhh.eeeee................eeeeeeeee........eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ww5 A  38 AAAYWDGDYYVKDDGSKAQSEWIFDNYYKAWFYINSDGRYSQNEWHGNYYLKSGGYMAQNEWIYDSNYKSWFYLKSDGAYAHQEWQLIGNKWYYFKKWGYMAKSQWQGSYFLNGQGAMIQNEWLYDPAYSAYFYLKSDGTYANQEWQKVGGKWYYFKKWGYMARNEWQGNYYLTGSGAMATDEVIMDGARYIFAASGELKEKKDLNVGWVHRDGKRYFFNNREEQVGTEHAKKIIDISEHNGRINDWKKVIDENEVDGVIVRLGYSGKEDKELAHNIKELNRLGIPYGVYLYTYAENETDAENDAKQTIELIKKYNMNLSYPIYYDVENWEYVNKSKRAPSDTDTWVKIINKYMDTMKQAGYQNVYVYSYRSLLQTRLKHPDILKHVNWVAAYTNALEWENPYYSGEKGWQYTSSEYMKGIQGRVDVSVWY 468
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467
   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 2WW5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WW5)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CW_binding_1] (12)

(-) Gene Ontology  (7, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8DP07_STRR6 | Q8DP07)
molecular function
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0003796    lysozyme activity    Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
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:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.

Chain A   (Q9Z4J8_STREE | Q9Z4J8)
molecular function
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0003796    lysozyme activity    Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
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:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.

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  2ww5
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9Z4J8_STREE | Q9Z4J8: 2wwc 2wwd
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        Q8DP07_STRR6 | Q8DP07: 2wwc 2wwd

(-) Related Entries Specified in the PDB File

2wwc 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH SYNTHETIC PEPTIDOGLYCAN LIGAND
2wwd 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH PNEUMMOCOCCAL PEPTIDOGLYCAN FRAGMENT