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(-) Description

Title :  STRUCTURE OF THE LDCB LD-CARBOXYPEPTIDASE REVEALS THE MOLECULAR BASIS OF PEPTIDOGLYCAN RECOGNITION
 
Authors :  C. N. Hoyland, C. Aldridge, R. M. Cleverley, K. Sidiq, M. C. Duchene, R. A W. Vollmer, R. J. Lewis
Date :  05 Feb 14  (Deposition) - 21 May 14  (Release) - 07 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,H
Biol. Unit 1:  A,H  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Las Family, Ld-Carboxypeptidase, Cell Wall Modifying Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. N. Hoyland, C. Aldridge, R. M. Cleverley, M. C. Duchene, G. Minasov, O. Onopriyenko, K. Sidiq, P. J. Stogios, W. F. Anderson, R. A. Daniel, A. Savchenko, W. Vollmer, R. J. Lewis
Structure Of The Ldcb Ld-Carboxypeptidase Reveals The Molecular Basis Of Peptidoglycan Recognition.
Structure V. 22 949 2014
PubMed-ID: 24909784  |  Reference-DOI: 10.1016/J.STR.2014.04.015

(-) Compounds

Molecule 1 - LDCB LD-CARBOXYPEPTIDASE
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 56-238
    Gene: SPR0554
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6
 
Molecule 2 - MUB-ALA-ZGL-LYS-DSG
    Chains: H
    Organism Scientific: LACTOBACILLUS ACIDOPHILUS
    Organism Taxid: 1579

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEH
Biological Unit 1 (1x): A    H
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 25)

Asymmetric Unit (7, 25)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DSG1Mod. Amino AcidD-ASPARAGINE
3LYS1Mod. Amino AcidLYSINE
4MG1Ligand/IonMAGNESIUM ION
5MUB1Mod. Amino AcidN-ACETYLMURAMIC ACID
6ZGL1Mod. Amino AcidD-ALPHA-GLUTAMINE
7ZN18Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DSG1Mod. Amino AcidD-ASPARAGINE
3LYS-1Mod. Amino AcidLYSINE
4MG-1Ligand/IonMAGNESIUM ION
5MUB1Mod. Amino AcidN-ACETYLMURAMIC ACID
6ZGL1Mod. Amino AcidD-ALPHA-GLUTAMINE
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DSG-1Mod. Amino AcidD-ASPARAGINE
3LYS1Mod. Amino AcidLYSINE
4MG-1Ligand/IonMAGNESIUM ION
5MUB-1Mod. Amino AcidN-ACETYLMURAMIC ACID
6ZGL-1Mod. Amino AcidD-ALPHA-GLUTAMINE
7ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DSG-1Mod. Amino AcidD-ASPARAGINE
3LYS-1Mod. Amino AcidLYSINE
4MG-1Ligand/IonMAGNESIUM ION
5MUB-1Mod. Amino AcidN-ACETYLMURAMIC ACID
6ZGL-1Mod. Amino AcidD-ALPHA-GLUTAMINE
7ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DSG-1Mod. Amino AcidD-ASPARAGINE
3LYS-1Mod. Amino AcidLYSINE
4MG-1Ligand/IonMAGNESIUM ION
5MUB-1Mod. Amino AcidN-ACETYLMURAMIC ACID
6ZGL-1Mod. Amino AcidD-ALPHA-GLUTAMINE
7ZN-1Ligand/IonZINC ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DSG-1Mod. Amino AcidD-ASPARAGINE
3LYS-1Mod. Amino AcidLYSINE
4MG-1Ligand/IonMAGNESIUM ION
5MUB-1Mod. Amino AcidN-ACETYLMURAMIC ACID
6ZGL-1Mod. Amino AcidD-ALPHA-GLUTAMINE
7ZN-1Ligand/IonZINC ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:153 , ASP A:160 , HIS A:207 , LYS H:4binding site for residue ZN A 301
02AC2SOFTWAREHIS A:-2 , GLU A:56 , HIS D:79binding site for residue ZN A 302
03AC3SOFTWAREASP A:62 , ASP A:85binding site for residue ZN A 303
04AC4SOFTWARESER A:121 , THR A:124binding site for residue MG A 304
05AC5SOFTWAREHIS B:153 , ASP B:160 , HIS B:207 , HOH B:409binding site for residue ZN B 301
06AC6SOFTWAREASP A:114 , HIS A:115 , HIS B:181 , ASP B:184binding site for residue ZN B 302
07AC7SOFTWAREHIS B:-2 , GLU B:56 , HOH B:410binding site for residue ZN B 303
08AC8SOFTWAREHIS B:79 , GLU B:232 , HOH B:416binding site for residue ZN B 304
09AC9SOFTWAREASP B:62 , ASP B:85 , ASP E:62 , ASP E:85binding site for residue ZN B 305
10AD1SOFTWAREHIS A:181 , ASP A:184 , SER B:113 , ASP B:114 , HIS B:115binding site for residue ZN B 306
11AD2SOFTWARELEU B:192 , GLY B:194 , GLU B:198 , THR B:199 , GLY B:200 , TYR B:201 , LEU C:168binding site for residue LYS B 307
12AD3SOFTWAREHIS C:153 , ASP C:160 , HIS C:207 , HOH C:406binding site for residue ZN C 301
13AD4SOFTWAREHIS C:79 , GLU C:232 , HIS E:-2 , GLU E:56binding site for residue ZN C 302
14AD5SOFTWAREHIS C:181 , HIS D:115binding site for residue ZN C 303
15AD6SOFTWAREASP C:114 , HIS C:115 , HIS D:181 , HOH D:408binding site for residue ZN C 304
16AD7SOFTWAREARG C:120 , ALA C:146binding site for residue CL C 305
17AD8SOFTWAREHIS D:153 , ASP D:160 , HIS D:207binding site for residue ZN D 301
18AD9SOFTWAREHIS A:79 , GLU A:232 , HIS D:-2 , GLU D:56binding site for residue ZN D 302
19AE1SOFTWAREHIS C:181binding site for residue CL D 303
20AE2SOFTWAREHIS E:153 , ASP E:160 , HIS E:207 , HOH E:411binding site for residue ZN E 301
21AE3SOFTWAREHOH C:407 , HIS E:79 , HOH E:412binding site for residue ZN E 302
22AE4SOFTWAREHIS E:115 , ASP E:131 , ASP E:180 , HIS E:181binding site for residue ZN E 303
23AE5SOFTWAREARG A:120 , GLN A:125 , ASP A:136 , TYR A:144 , SER A:145 , ALA A:146 , SER A:151 , HIS A:153 , ASP A:160 , TYR A:191 , TYR A:201 , MET A:202 , ALA A:203 , GLU A:204 , HIS A:207 , ZN A:301 , ASP C:85 , ASN C:87 , PRO C:88 , HOH H:101binding site for chain H of MUB-ALA-ZGL-LYS-DSG

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:165 -Gly A:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OXD)

(-) 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:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eeee....eeee...............hhhhhhhhhhhhhhhhhhh......ee...hhhhhhhhhhhhhhhhh.............hhhhhh.eeee......hhhhhhhhhhhhhhhhhh.eee.....hhhhhh......eeee...hhhhhhhhh.hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oxd A  -3 SHMEVVNKGDYYSIQGKYDEIIVANKHYPLSKDYNPGENPTAKAELVKLIKAMQEAGFPISDHYSGFRSYETQTKLYQDYVNQDGKEAADRYSARPGYSEHQTGLAFDVIGTDGDLVTEEKAAQWLLDHAADYGFVVRYLKGKEKETGYMAEEWHLRYVGKEAKEIAESGLSLEEYYGFEGGDYV 237
                              ||    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     
                             -1|                                                                                                                                                                                     
                              56                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eeee....eeee...............hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..eee......hhhhhhhhhhhhhhhhhh.eee..............eeee...hhhhhhhhh.hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oxd B  -3 SHMEVVNKGDYYSIQGKYDEIIVANKHYPLSKDYNPGENPTAKAELVKLIKAMQEAGFPISDHYSGFRSYETQTKLYQDYVNQDGKEAADRYSARPGYSEHQTGLAFDVIGTDDLVTEEKAAQWLLDHAADYGFVVRYLKGETGYMAEEWHLRYVGKEAKEIAESGLSLEEYYGFEGGDYV 237
                              ||    62        72        82        92       102       112       122       132       142       152       162  ||   173       183       193||     206       216       226       236 
                             -1|                                                                                                          165|                        194|                                       
                              56                                                                                                           167                         198                                       


Chain C from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeee....eeee...............hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh.......hhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh.eee.....hhhhhh......eeee...hhhhhhhhh.hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oxd C  56 EVVNKGDYYSIQGKYDEIIVANKHYPLSKDYNPGENPTAKAELVKLIKAMQEAGFPISDHYSGFRSYETQTKLYSARPGYSEHQTGLAFDVIGTDGDLVTEEKAAQWLLDHAADYGFVVRYLKGKEKETGYMAEEWHLRYVGKEAKEIAESGLSLEEYYGFEGGDYV 237
                                    65        75        85        95       105       115       125   ||  150       160       170       180       190       200       210       220       230       
                                                                                                   129|                                                                                            
                                                                                                    145                                                                                            


Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee....eeee...............hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh......hhhhhh.eeeeee....hhhhhhhhhhhhhhhhhh.eee.....hhhhhh......eeee...hhhhhhhhh.hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oxd D  -2 HMEVVNKGDYYSIQGKYDEIIVANKHYPLSKDYNPGENPTAKAELVKLIKAMQEAGFPISDHYSGFRSYETQTKLYQDSARPGYSEHQTGLAFDVIGTDGDLVTEEKAAQWLLDHAADYGFVVRYLKGKEKETGYMAEEWHLRYVGKEAKEIAESGLSLEEYYGFEGGDYV 237
                             ||     63        73        83        93       103       113       123       146       156       166       176       186       196       206       216       226       236 
                            -1|                                                                        131|                                                                                            
                             56                                                                         145                                                                                            


Chain E from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee....eeee...............hhhhhhhhhhhhhhhhhh............hhhhhhhhhh..hhhhh.....hhhhh..eee.......hhhhhhhhhhhhh.eee.....hhhhhh......eeee...hhhhhhhhh.hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oxd E  -2 HMEVVNKGDYYSIQGKYDEIIVANKHYPLSKDYNPGENPTAKAELVKLIKAMQEAGFPISDHYSGFRSYETQTKLYQDAADRYSARPGYSEHQTGLAFDVIGTDGEKAAQWLLDHAADYGFVVRYLKGKEKETGYMAEEWHLRYVGKEAKEIAESGLSLEEYYGFEGGDYV 237
                             ||     63        73        83        93       103       113       123       141       151       161    || 176       186       196       206       216       226       236 
                            -1|                                                                        131|                       166|                                                                 
                             56                                                                         140                        172                                                                 


Chain H from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4oxd H   1 xAxKx   5
                            | | |
                            1-MUB
                              3-ZGL
                                5-DSG
   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 4OXD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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  Q8DQQ1_STRR6 | Q8DQQ1
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 Related Entries

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

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        Q8DQQ1_STRR6 | Q8DQQ1: 4ox5

(-) Related Entries Specified in the PDB File

4ox3
4ox5 4OX5 CONTAINS THE APO PROTEIN, WITHOUT LIGAND.