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(-) Description

Title :  THE STRUCTURE OF A FAMILY GH25 LYSOZYME FROM ASPERGILLUS FUMIGATUS
 
Authors :  J. E. Korczynska, S. Danielsen, U. Schagerlof, J. P. Turkenburg, G. J. D K. S. Wilson, E. J. Taylor
Date :  11 Mar 10  (Deposition) - 08 Sep 10  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Peptidoglycan Cleavage, Endo-N-Acetylmuramidases, Hydrolase, Dxe Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. E. Korczynska, S. Danielsen, U. Schagerlof, J. P. Turkenburg, G. J. Davies, K. S. Wilson, E. J. Taylor
The Structure Of A Family Gh25 Lysozyme From Aspergillus Fumigatus
Acta Crystallogr. , Sect. F V. 66 973 2010
PubMed-ID: 20823508  |  Reference-DOI: 10.1107/S1744309110025601

(-) Compounds

Molecule 1 - GLYCOSYL HYDROLASE
    ChainsA, B, C, D, E, F
    EC Number3.2.1.17
    FragmentRESIDUES 26-235
    Organism ScientificASPERGILLUS FUMIGATUS
    Organism Taxid330879
    StrainAF293
    SynonymFAMILY 25 PEPTIDOGLYCAN HYDROLASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A     
Biological Unit 2 (1x) B    
Biological Unit 3 (1x)  C   
Biological Unit 4 (1x)   D  
Biological Unit 5 (1x)    E 
Biological Unit 6 (1x)     F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:109 , CYS A:115 , TRP A:150 , THR D:50BINDING SITE FOR RESIDUE CL A1219
2AC2SOFTWAREASN B:109 , CYS B:115 , TRP B:150 , THR E:50BINDING SITE FOR RESIDUE CL B1219
3AC3SOFTWARETHR B:50 , ASN C:109 , CYS C:115 , TRP C:150BINDING SITE FOR RESIDUE CL C1219
4AC4SOFTWAREASN D:109 , CYS D:115 , TRP D:150 , HOH F:2036BINDING SITE FOR RESIDUE CL D1219
5AC5SOFTWAREHOH C:2052 , TYR E:108 , ASN E:109 , CYS E:115 , TRP E:150BINDING SITE FOR RESIDUE CL E1219
6AC6SOFTWARETHR A:50 , ASN F:109 , CYS F:115 , TRP F:150BINDING SITE FOR RESIDUE CL F1219

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:115 -A:154
2B:115 -B:154
3C:115 -C:154
4D:115 -D:154
5E:115 -E:154
6F:115 -F:154

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X8R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X8R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X8R)

(-) Exons   (0, 0)

(no "Exon" information available for 2X8R)

(-) 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:209
 aligned with A4DA29_ASPFU | A4DA29 from UniProtKB/TrEMBL  Length:235

    Alignment length:209
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226         
         A4DA29_ASPFU    27 TTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 235
               SCOP domains d2x8ra_ A: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains 2x8rA00 A:10-218 Glycosidases                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......hhhhhhhh.eeeeeeeeee.......hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh..............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh..........eeee..................eeeee.......eeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x8r A  10 TTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 218
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with A4DA29_ASPFU | A4DA29 from UniProtKB/TrEMBL  Length:235

    Alignment length:210
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235
         A4DA29_ASPFU    26 ATTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 235
               SCOP domains d2x8rb_ B: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 2x8rB00 B:9-218 Glycosidases                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhh...eeeeeeee.......hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh..............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh..........eeee..................eeeee.......eeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x8r B   9 ATTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 218
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218

Chain C from PDB  Type:PROTEIN  Length:210
 aligned with A4DA29_ASPFU | A4DA29 from UniProtKB/TrEMBL  Length:235

    Alignment length:210
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235
         A4DA29_ASPFU    26 ATTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 235
               SCOP domains d2x8rc_ C: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 2x8rC00 C:9-218 Glycosidases                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhh.............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh..........eeee..................eeeee.......eeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x8r C   9 ATTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 218
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218

Chain D from PDB  Type:PROTEIN  Length:209
 aligned with A4DA29_ASPFU | A4DA29 from UniProtKB/TrEMBL  Length:235

    Alignment length:209
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226         
         A4DA29_ASPFU    27 TTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 235
               SCOP domains d2x8rd_ D: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains 2x8rD00 D:10-218 Glycosidases                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh..............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh..........eeee..................eeeee.......eeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x8r D  10 TTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 218
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         

Chain E from PDB  Type:PROTEIN  Length:210
 aligned with A4DA29_ASPFU | A4DA29 from UniProtKB/TrEMBL  Length:235

    Alignment length:210
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235
         A4DA29_ASPFU    26 ATTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 235
               SCOP domains d2x8re_ E: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 2x8rE00 E:9-218 Glycosidases                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhh.............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh..........eeee..................eeeee.......eeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x8r E   9 ATTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 218
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218

Chain F from PDB  Type:PROTEIN  Length:209
 aligned with A4DA29_ASPFU | A4DA29 from UniProtKB/TrEMBL  Length:235

    Alignment length:209
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226         
         A4DA29_ASPFU    27 TTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 235
               SCOP domains d2x8rf_ F: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains 2x8rF00 F:10-218 Glycosidases                                                                                                                                                                                     CATH domains
           Pfam domains (1) -----Glyco_hydro_25-2x8rF01 F:15-201                                                                                                                                                            ----------------- Pfam domains (1)
           Pfam domains (2) -----Glyco_hydro_25-2x8rF02 F:15-201                                                                                                                                                            ----------------- Pfam domains (2)
           Pfam domains (3) -----Glyco_hydro_25-2x8rF03 F:15-201                                                                                                                                                            ----------------- Pfam domains (3)
           Pfam domains (4) -----Glyco_hydro_25-2x8rF04 F:15-201                                                                                                                                                            ----------------- Pfam domains (4)
           Pfam domains (5) -----Glyco_hydro_25-2x8rF05 F:15-201                                                                                                                                                            ----------------- Pfam domains (5)
           Pfam domains (6) -----Glyco_hydro_25-2x8rF06 F:15-201                                                                                                                                                            ----------------- Pfam domains (6)
         Sec.struct. author .eeeeeee.......hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhh.............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh..........eeee..................eeeee.......eeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x8r F  10 TTVQGFDISNHQKSVNFEAAKKDGAQFVMIKATEGTTYKDTVFNSHYTGATKAGLLRGGYHFARPDKSTGSTQAKFFLKNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQMVAWIHDFVNEYHHATSRWPMIYTTADWWNRCTGNAKGFGDKCPLVLAAYSSSPPKTIPGDWKTWTIWQNSDKYKHGGDSDKFNGPMTQLRKLASG 218
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         

   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  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 6)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (A4DA29_ASPFU | A4DA29)
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: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: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.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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