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(-) Description

Title :  LYTM DOMAIN OF ENVC, AN ACTIVATOR OF CELL WALL AMIDASES IN ESCHERICHIA COLI
 
Authors :  C. Morlot, N. T. Peters, D. C. Yang, T. Uehara, T. Vernet, T. G. Bernhardt
Date :  29 Mar 13  (Deposition) - 03 Jul 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Cell Cycle, Amidase Activator, Autolysin, Cytokinesis, Morphogenesis, Sacculus, Peptidoglycan (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. T. Peters, C. Morlot, D. C. Yang, T. Uehara, T. Vernet, T. G. Bernhard
Structure-Function Analysis Of The Lytm Domain Of Envc, An Activator Of Cell Wall Remodeling At The Escherichia Coli Division Site.
Mol. Microbiol. V. 89 690 2013
PubMed-ID: 23796240  |  Reference-DOI: 10.1111/MMI.12304

(-) Compounds

Molecule 1 - MUREIN HYDROLASE ACTIVATOR ENVC
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTB104
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: LYTM DOMAIN, RESIDUES 278-419
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: SEPTAL RING FACTOR

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 30)

Asymmetric Unit (4, 30)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3IOD23Ligand/IonIODIDE ION
4K1Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3IOD4Ligand/IonIODIDE ION
4K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3IOD8Ligand/IonIODIDE ION
4K-1Ligand/IonPOTASSIUM ION
Biological Unit 3 (2, 7)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3IOD6Ligand/IonIODIDE ION
4K-1Ligand/IonPOTASSIUM ION
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3IOD5Ligand/IonIODIDE ION
4K-1Ligand/IonPOTASSIUM ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:410 , ARG D:405BINDING SITE FOR RESIDUE IOD A1420
02AC2SOFTWAREIOD B:1421BINDING SITE FOR RESIDUE IOD A1421
03AC3SOFTWAREGLN A:348 , HOH D:2045BINDING SITE FOR RESIDUE IOD A1422
04AC4SOFTWAREGLY A:339 , ARG A:340BINDING SITE FOR RESIDUE IOD A1423
05AC5SOFTWARETRP A:346 , GLY A:349 , GLY A:351BINDING SITE FOR RESIDUE CL A1424
06AC6SOFTWAREIOD B:1500BINDING SITE FOR RESIDUE IOD B1420
07AC7SOFTWAREIOD A:1421 , ALA B:293 , ARG B:406BINDING SITE FOR RESIDUE IOD B1421
08AC8SOFTWAREALA B:410 , ARG C:405BINDING SITE FOR RESIDUE IOD B1422
09AC9SOFTWAREGLN B:379BINDING SITE FOR RESIDUE IOD B1423
10BC1SOFTWARETRP B:346 , GLN B:348 , GLY B:349 , GLY B:351BINDING SITE FOR RESIDUE CL B1424
11BC2SOFTWAREALA A:293 , ARG A:406 , IOD B:1420BINDING SITE FOR RESIDUE IOD B1500
12BC3SOFTWARETRP D:300BINDING SITE FOR RESIDUE IOD B1501
13BC4SOFTWAREGLN C:313 , GLY C:316BINDING SITE FOR RESIDUE IOD B1503
14BC5SOFTWAREALA C:293 , ARG C:406 , IOD D:1420BINDING SITE FOR RESIDUE IOD C1420
15BC6SOFTWARESER C:391 , IOD C:1500BINDING SITE FOR RESIDUE IOD C1421
16BC7SOFTWAREGLN B:348BINDING SITE FOR RESIDUE IOD C1422
17BC8SOFTWARESER C:328 , GLU C:329BINDING SITE FOR RESIDUE IOD C1423
18BC9SOFTWAREHOH C:2013BINDING SITE FOR RESIDUE IOD C1424
19CC1SOFTWARETRP C:346 , GLN C:348 , GLY C:349 , GLY C:351 , SER C:392BINDING SITE FOR RESIDUE CL C1425
20CC2SOFTWAREGLN B:407 , GLY B:408 , LYS C:321 , TYR C:350 , GLU C:403 , ARG C:405BINDING SITE FOR RESIDUE GOL C1426
21CC3SOFTWAREIOD C:1421 , ARG D:406BINDING SITE FOR RESIDUE IOD C1500
22CC4SOFTWAREIOD C:1420 , SER D:391 , SER D:392BINDING SITE FOR RESIDUE IOD D1420
23CC5SOFTWAREGLN D:313 , GLY D:316BINDING SITE FOR RESIDUE IOD D1421
24CC6SOFTWAREARG B:340 , THR D:306BINDING SITE FOR RESIDUE IOD D1422
25CC7SOFTWAREHOH B:2027 , SER D:328 , GLU D:329BINDING SITE FOR RESIDUE IOD D1423
26CC8SOFTWARETRP D:346 , GLN D:348 , GLY D:349 , GLY D:351 , SER D:392BINDING SITE FOR RESIDUE CL D1424
27CC9SOFTWAREGLN A:407 , GLY A:408 , HOH A:2111 , LYS D:321 , TYR D:350 , GLU D:403 , ARG D:405 , HOH D:2080BINDING SITE FOR RESIDUE GOL D1425
28DC1SOFTWAREGLN A:348BINDING SITE FOR RESIDUE IOD D1500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BH5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BH5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BH5)

(-) Exons   (0, 0)

(no "Exon" information available for 4BH5)

(-) 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:130
 aligned with ENVC_ECOLI | P37690 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:130
                                   299       309       319       329       339       349       359       369       379       389       399       409       419
           ENVC_ECOLI   290 GLGAPRGQAFWPVRGPTLHRYGEQLQGELRWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGSQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQPWLGR 419
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee....eee..ee...eeee.....eee....eeeeeeee.....eeeeeeee..eeeeeeeeeee......ee....eeeee.........eeeeeeee..eee.hhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bh5 A 290 GLGAPRGQAFWPVRGPTLHRYGEQLQGELRWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGSQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQPWLGR 419
                                   299       309       319       329       339       349       359       369       379       389       399       409       419


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with ENVC_ECOLI | P37690 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:130
                                   299       309       319       329       339       349       359       369       379       389       399       409       419
           ENVC_ECOLI   290 GLGAPRGQAFWPVRGPTLHRYGEQLQGELRWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGSQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQPWLGR 419
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee....eee..ee...eeee.....eee....eeeeeeee.....eeeeeeee..eeeeeeee.ee......ee....eeee..........eeeeeeee..eee.hhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bh5 B 290 GLGAPRGQAFWPVRGPTLHRYGEQLQGELRWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGSQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQPWLGR 419
                                   299       309       319       329       339       349       359       369       379       389       399       409       419


Chain C from PDB  Type:PROTEIN  Length:130
 aligned with ENVC_ECOLI | P37690 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:130
                                   299       309       319       329       339       349       359       369       379       389       399       409       419
           ENVC_ECOLI   290 GLGAPRGQAFWPVRGPTLHRYGEQLQGELRWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGSQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQPWLGR 419
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee....eee..ee...eeee.....eee....eeeeeeeee...eeeeeeeee..eeeeeeee.ee......ee....eeee..........eeeeeeee..eee.hhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bh5 C 290 GLGAPRGQAFWPVRGPTLHRYGEQLQGELRWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGSQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQPWLGR 419
                                   299       309       319       329       339       349       359       369       379       389       399       409       419


Chain D from PDB  Type:PROTEIN  Length:130
 aligned with ENVC_ECOLI | P37690 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:130
                                   299       309       319       329       339       349       359       369       379       389       399       409       419
           ENVC_ECOLI   290 GLGAPRGQAFWPVRGPTLHRYGEQLQGELRWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGSQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQPWLGR 419
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee....eee..ee...eeee.....eee....eeeeeeee.....eeeeeeee..eeeeeeee.ee......ee....eeee..........eeeeeeee..eee.hhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bh5 D 290 GLGAPRGQAFWPVRGPTLHRYGEQLQGELRWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGSQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQPWLGR 419
                                   299       309       319       329       339       349       359       369       379       389       399       409       419
   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 4BH5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BH5)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ENVC_ECOLI | P37690)
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.
biological process
    GO:0001896    autolysis    A programmed cell death process observed in bacteria and filamentous fungi and leading to spontaneous death by lysis. Examples are lysis of the mother cell during sporulation of Bacillus subtilis and self-degradation of fungal cells in Aspergillus nidulans. Autolysis is also involved in bacterial biofilm formation.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0000920    cell separation after cytokinesis    The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components.
    GO:0009273    peptidoglycan-based cell wall biogenesis    The chemical reactions and pathways resulting in the formation of the peptidoglycan-based cell wall. An example of this process is found in Escherichia coli.
    GO:0051345    positive regulation of hydrolase activity    Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
cellular component
    GO:0032153    cell division site    The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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