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(-) Description

Title :  CRYSTAL STRUCTURE OF TYPE VI PEPTIDOGLYCAN MURAMIDASE EFFECTOR TSE3 IN COMPLEX WITH ITS COGNATE IMMUNITY PROTEIN TSI3
 
Authors :  J. Ding, T. Wang, W. Liu, D. C. Wang
Date :  26 Apr 13  (Deposition) - 02 Oct 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Protein Complex, Muramidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wang, J. Ding, Y. Zhang, D. C. Wang, W. Liu
Complex Structure Of Type Vi Peptidoglycan Muramidase Effector And A Cognate Immunity Protein
Acta Crystallogr. , Sect. D V. 69 1889 2013
PubMed: search  |  Reference-DOI: 10.1107/S090744491301576X

(-) Compounds

Molecule 1 - TYPE VI SECRETION EXPORTED 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PA3484
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
 
Molecule 2 - TSE3-SPECIFIC IMMUNITY PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PA3485
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2EDO8Ligand/Ion1,2-ETHANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:282 , THR A:285 , TYR A:326 , TYR A:376 , HOH A:631 , GLY B:98 , SER B:99BINDING SITE FOR RESIDUE EDO A 501
02AC2SOFTWARETYR A:289 , ARG A:325 , TYR A:329 , HOH A:871BINDING SITE FOR RESIDUE EDO A 502
03AC3SOFTWAREGLN A:165 , LEU A:168 , GLN A:264 , ALA A:265 , HOH A:644 , HOH A:942BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREASN A:181 , ASP A:253 , GLN A:254 , GLU A:258 , GLN A:280 , HOH A:601 , HOH A:602BINDING SITE FOR RESIDUE CA A 504
05AC5SOFTWAREGLU A:258 , ASP A:262 , SER A:275 , GLN A:280 , GLU B:126BINDING SITE FOR RESIDUE CA A 505
06AC6SOFTWAREGLU A:375 , SER A:378 , ARG A:379 , ASP A:382 , ASN A:384 , HOH A:603BINDING SITE FOR RESIDUE CA A 506
07AC7SOFTWARETYR A:81 , HOH A:689 , HOH A:795 , THR B:27 , LEU B:28 , THR B:29 , EDO B:202BINDING SITE FOR RESIDUE EDO B 201
08AC8SOFTWARETHR A:77 , LEU B:28 , THR B:29 , ARG B:46 , PHE B:51 , EDO B:201BINDING SITE FOR RESIDUE EDO B 202
09AC9SOFTWAREARG B:52 , GLN B:64 , ARG B:105 , SER B:120 , ALA B:121 , SER B:122 , HOH B:404 , HOH B:429BINDING SITE FOR RESIDUE EDO B 203
10BC1SOFTWAREPRO A:350 , SER A:351 , ASP A:367 , ARG A:370 , HOH B:350BINDING SITE FOR RESIDUE EDO B 204
11BC2SOFTWARETYR B:90 , THR B:131 , TRP B:136 , HOH B:352 , HOH B:391BINDING SITE FOR RESIDUE EDO B 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WA5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:60 -Pro A:61
2Gly A:134 -Val A:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WA5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WA5)

(-) Exons   (0, 0)

(no "Exon" information available for 3WA5)

(-) 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:400
 aligned with Q9HYC5_PSEAE | Q9HYC5 from UniProtKB/TrEMBL  Length:408

    Alignment length:407
                                    11        21        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       381       391       401       
         Q9HYC5_PSEAE     2 TATSDLIESLISYSWDDWQVTRQEARRVIAAIRNDNVPDATIAALDKSGSLIKLFQRVGPPELARSLIASIAGRTTMQRYQARNALIRSLINNPLGTQTDNWIYFPTITFFDICADLADAAGRLGFAAAGATGVASQAIQGPFSGVGATGVNPTDLPSIAFGDQLKLLNKDPATVTKYSNPLGDLGAYLSQLSPQDKLNQAQTLVGQPISTLFPDAYPGNPPSRAKVMSAAARKYDLTPQLIGAIILAEQRDQTRDEDAKDYQAAVSIKSANTSIGLGQVVVSTAIKYELFTDLLGQPVRRGLSRKAVATLLASDEFNIFATARYIRYVANLASQQDLRKLPKTRGAFPSIDLRAYAGNPRNWPRDNVRALASEYTSRPWDDNLSPGWPMFVDDAYATFLDPGMRFP 408
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.-------..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh........hhhhh..hhhhhhhhhhhhhhhhhhhh...................hhhhhh.hhhhh...hhhhhhhhhh.hhhhhhhh.....hhhhhhhh.hhhhhhhhhhhhhhh.....hhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......ee....eehhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wa5 A   2 TATSDLIESLI-------QVTRQEARRVIAAIRNDNVPDATIAALDKSGSLIKLFQRVGPPELARSLIASIAGRTTmQRYQARNALIRSLINNPLGTQTDNWIYFPTITFFDICADLADAAGRLGFAAAGATGVASQAIQGPFSGVGATGVNPTDLPSIAFGDQLKLLNKDPATVTKYSNPLGDLGAYLSQLSPQDKLNQAQTLVGQPISTLFPDAYPGNPPSRAKVmSAAARKYDLTPQLIGAIILAEQRDQTRDEDAKDYQAAVSIKSANTSIGLGQVVVSTAIKYELFTDLLGQPVRRGLSRKAVATLLASDEFNIFATARYIRYVANLASQQDLRKLPKTRGAFPSIDLRAYAGNPRNWPRDNVRALASEYTSRPWDDNLSPGWPmFVDDAYATFLDPGmRFP 408
                                    11|       21        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       381       391       401   |   
                                     12      20                                                        78-MSE                                                                                                                                                229-MSE                                                                                                                                                           391-MSE       405-MSE


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with Q9HYC4_PSEAE | Q9HYC4 from UniProtKB/TrEMBL  Length:145

    Alignment length:124
                                    31        41        51        61        71        81        91       101       111       121       131       141    
         Q9HYC4_PSEAE    22 VDFDKTLTHPNGLVVERPVGFDARRSAEGFRFDEGGKLRNPRQLEVQRQDAPPPPDLASRRLGDGEARYKVEEDDGGSAGSEYRLWAAKPAGARWIVVSASEQSEDGEPTFALAWALLERARLQ 145
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee..eeeee...eeeeee........eeeeeee........eeeee..eeeeeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeee......hhhhhhhhhhhee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wa5 B  22 VDFDKTLTHPNGLVVERPVGFDARRSAEGFRFDEGGKLRNPRQLEVQRQDAPPPPDLASRRLGDGEARYKVEEDDGGSAGSEYRLWAAKPAGARWIVVSASEQSEDGEPTFALAWALLERARLQ 145
                                    31        41        51        61        71        81        91       101       111       121       131       141
   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 3WA5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WA5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WA5)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9HYC5_PSEAE | Q9HYC5)
molecular function
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

Chain B   (Q9HYC4_PSEAE | Q9HYC4)

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  Cis Peptide Bonds
    Gly A:134 - Val A:135   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q9HYC4_PSEAE | Q9HYC4: 4luq 4m5f 4n7s 4n80 4n88
        Q9HYC5_PSEAE | Q9HYC5: 4luq 4m5e 4m5f 4n7s 4n80 4n88

(-) Related Entries Specified in the PDB File

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