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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF BOVINE STOMACH LYSOZYME
 
Authors :  D. Akieda, Y. Nonaka, N. Watanabe, I. Tanaka, M. Kamiya, T. Aizawa, K. Nitta, M. Demura, K. Kawano
Date :  21 May 07  (Deposition) - 27 May 08  (Release) - 27 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Lysozyme C, Stomach Lysozyme, 1, 4-Beta-N-Acetylmuramidase C, Bacteriolytic Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Akieda, Y. Nonaka, N. Watanabe, I. Tanaka, M. Kamiya, T. Aizawa, K. Nitta, M. Demura, K. Kawano
Stability Of Bovine Stomach Lysozyme In Acidic Condition
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSOZYME C-2
    Chains: A
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Common: FUNGI
    Expression System Plasmid: PPIC3
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: LYSOZYME 2, 1,4-BETA-N-ACETYLMURAMIDASE C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:61 , CYS A:65 , ALA A:73 , HOH A:2002 , HOH A:2008BINDING SITE FOR RESIDUE NA A 2001
2AC2SOFTWAREARG A:5 , LYS A:33 , CYS A:77 , HIS A:78 , ALA A:94 , HOH A:2050 , HOH A:2128 , HOH A:2134BINDING SITE FOR RESIDUE MPD A 1001
3AC3SOFTWARETYR A:20 , HIS A:98 , SER A:101 , SER A:122 , HOH A:2019 , HOH A:2086BINDING SITE FOR RESIDUE MPD A 1002

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:127
2A:30 -A:115
3A:65 -A:81
4A:77 -A:95

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z2F)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LACTALBUMIN_LYSOZYME_2PS51348 Alpha-lactalbumin / lysozyme C family profile.LYSC2_BOVIN19-147  1A:1-129
2LACTALBUMIN_LYSOZYME_1PS00128 Alpha-lactalbumin / lysozyme C signature.LYSC2_BOVIN95-113  1A:77-95

(-) Exons   (0, 0)

(no "Exon" information available for 2Z2F)

(-) 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:129
 aligned with LYSC2_BOVIN | Q06283 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:129
                                    28        38        48        58        68        78        88        98       108       118       128       138         
          LYSC2_BOVIN    19 KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKTPNAVDGCHVSCSELMENDIAKAVACAKHIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL 147
               SCOP domains d2z2fa_ A: automated matches                                                                                                      SCOP domains
               CATH domains 2z2fA00 A:1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
               Pfam domains Lys-2z2fA01 A:1-127                                                                                                            -- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeee....eeee....ee...................hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: A:1-129 UniProt: 19-147                                                                              PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------LACTALBUMIN_LYSOZYM---------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z2f A   1 KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKTPNAVDGCHVSCSELMENDIAKAVACAKHIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL 129
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Lysozyme (266)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LYSC2_BOVIN | Q06283)
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: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:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0007586    digestion    The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    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.

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  2z2f
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