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(-) Description

Title :  3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH SYNTHETIC PEPTIDOGLYCAN LIGAND
 
Authors :  I. Perez-Dorado, R. Sanles, J. A. Hermoso, A. Gonzalez, A. Garcia, P. Ga J. L. Garcia
Date :  22 Oct 09  (Deposition) - 21 Apr 10  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
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, 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
    Mutation: YES
    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  (2, 22)

Asymmetric/Biological Unit (2, 22)
No.NameCountTypeFull Name
1CHT8Ligand/IonCHOLINE ION
2GOL14Ligand/IonGLYCEROL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:41 , TRP A:42 , ASP A:62 , HOH A:2488BINDING SITE FOR RESIDUE GOL A 601
02AC2SOFTWAREASN A:72 , ASP A:74 , ARG A:76 , TYR A:77 , GLU A:81 , ARG A:408 , GLN A:412BINDING SITE FOR RESIDUE GOL A 602
03AC3SOFTWAREILE A:100 , TYR A:101 , HOH A:2489 , HOH A:2490BINDING SITE FOR RESIDUE GOL A 603
04AC4SOFTWARETRP A:135 , TYR A:137 , GLU A:260 , HOH A:2296 , HOH A:2491BINDING SITE FOR RESIDUE GOL A 604
05AC5SOFTWARETYR A:117 , HIS A:119 , LYS A:134 , TRP A:135 , ARG A:227 , HOH A:2061BINDING SITE FOR RESIDUE GOL A 605
06AC6SOFTWARETRP A:122 , GLN A:144 , GLY A:145 , SER A:146 , TYR A:147 , HOH A:2493BINDING SITE FOR RESIDUE GOL A 606
07AC7SOFTWAREASN A:127 , LYS A:128 , TRP A:129 , GLN A:157 , HOH A:2494BINDING SITE FOR RESIDUE GOL A 607
08AC8SOFTWAREGLN A:142 , TRP A:143 , ASP A:163 , ALA A:165BINDING SITE FOR RESIDUE GOL A 608
09AC9SOFTWARETRP A:204 , GLY A:206BINDING SITE FOR RESIDUE GOL A 609
10BC1SOFTWAREARG A:253 , GLU A:266 , ASP A:294 , HOH A:2306 , HOH A:2307 , HOH A:2495BINDING SITE FOR RESIDUE GOL A 610
11BC2SOFTWAREHIS A:267 , LYS A:269 , GLU A:444 , TRP A:467 , TYR A:468 , HOH A:2300BINDING SITE FOR RESIDUE GOL A 611
12BC3SOFTWAREASN A:258 , TYR A:430 , TYR A:449 , THR A:450 , HOH A:2251 , HOH A:2497 , HOH A:2498 , HOH A:2499BINDING SITE FOR RESIDUE GOL A 612
13BC4SOFTWARELYS A:269 , SER A:357 , TYR A:358 , GLU A:444 , HOH A:2417 , HOH A:2500BINDING SITE FOR RESIDUE GOL A 613
14BC5SOFTWAREASP A:273 , ASP A:363 , GLN A:365 , TYR A:405 , GLN A:448 , ASP A:463 , HOH A:2395 , HOH A:2501 , HOH A:2502BINDING SITE FOR RESIDUE GOL A 614
15BC6SOFTWARETRP A:42 , TYR A:65 , PHE A:69 , TYR A:77 , GLY A:91 , TYR A:93BINDING SITE FOR RESIDUE CHT A 701
16BC7SOFTWARETRP A:59 , TRP A:68 , TYR A:86 , MET A:94 , ASP A:114BINDING SITE FOR RESIDUE CHT A 702
17BC8SOFTWARETRP A:82 , GLY A:84 , TYR A:105 , PHE A:109 , TYR A:117 , TRP A:135 , HOH A:2503BINDING SITE FOR RESIDUE CHT A 703
18BC9SOFTWARETRP A:99 , TRP A:108 , TYR A:130 , MET A:138 , GLN A:152BINDING SITE FOR RESIDUE CHT A 704
19CC1SOFTWARETRP A:122 , TRP A:129 , TYR A:147 , ASP A:175BINDING SITE FOR RESIDUE CHT A 705
20CC2SOFTWARETRP A:143 , GLY A:145 , TYR A:166 , PHE A:170 , TYR A:178 , TRP A:196BINDING SITE FOR RESIDUE CHT A 706
21CC3SOFTWARETYR A:169 , TYR A:191 , MET A:199 , SER A:213BINDING SITE FOR RESIDUE CHT A 707
22CC4SOFTWARETYR A:302 , TYR A:369 , VAL A:370BINDING SITE FOR RESIDUE CHT A 708

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WWC)

(-) 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_1-2wwcA0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2wwcA0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2wwcA0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2wwcA0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 2wwc A  38 AAAYWDGDYYVKDDGSKAQSEWIFDNYYKAWFYINSDGRYSQNEWHGNYYLKSGGYMAQNEWIYDSNYKSWFYLKSDGAYAHQEWQLIGNKWYYFKKWGYMAKSQWQGSYFLNGQGAMIQNEWLYDPAYSAYFYLKSDGTYANQEWQKVGGKWYYFKKWGYMARNEWQGNYYLTGSGAMATDEVIMDGARYIFAASGELKEKKDLNVGWVHRDGKRYFFNNREEQVGTEHAKKIIDISEHNGRINDWKKVIDENEVDGVIVRLGYSGKEDKELAHNIKELNRLGIPYGVYLYTYAENETDAENDAKQTIELIKKYNMNLSYPIYYDVQNWEYVNKSKRAPSDTDTWVKIINKYMDTMKQAGYQNVYVYSYRSLLQTRLKHPDILKHVNWVAAYTNALEWENPYYSGEKGWQYTSSEYMKGIQGRVDVSVWY 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_1-2wwcA0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2wwcA0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2wwcA0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2wwcA0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 2wwc A  38 AAAYWDGDYYVKDDGSKAQSEWIFDNYYKAWFYINSDGRYSQNEWHGNYYLKSGGYMAQNEWIYDSNYKSWFYLKSDGAYAHQEWQLIGNKWYYFKKWGYMAKSQWQGSYFLNGQGAMIQNEWLYDPAYSAYFYLKSDGTYANQEWQKVGGKWYYFKKWGYMARNEWQGNYYLTGSGAMATDEVIMDGARYIFAASGELKEKKDLNVGWVHRDGKRYFFNNREEQVGTEHAKKIIDISEHNGRINDWKKVIDENEVDGVIVRLGYSGKEDKELAHNIKELNRLGIPYGVYLYTYAENETDAENDAKQTIELIKKYNMNLSYPIYYDVQNWEYVNKSKRAPSDTDTWVKIINKYMDTMKQAGYQNVYVYSYRSLLQTRLKHPDILKHVNWVAAYTNALEWENPYYSGEKGWQYTSSEYMKGIQGRVDVSVWY 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 2WWC)

(-) CATH Domains  (0, 0)

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

(-) 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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  2wwc
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9Z4J8_STREE | Q9Z4J8: 2ww5 2wwd
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        Q8DP07_STRR6 | Q8DP07: 2ww5 2wwd

(-) Related Entries Specified in the PDB File

2ww5 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS PNEUMONIAE AT 1.6 A RESOLUTION
2wwd 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH PNEUMMOCOCCAL PEPTIDOGLYCAN FRAGMENT