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(-) Description

Title :  CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TETRASACCHARIDE PENTAPEPTIDE
 
Authors :  C. Artola-Recolons, J. A. Hermoso
Date :  10 Jul 13  (Deposition) - 09 Oct 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Keywords :  Hydrolase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lee, C. Artola-Recolons, C. Carrasco-Lopez, S. Martinez-Caballero, D. Hesek, E. Spink, E. Lastochkin, W. Zhang, L. M. Hellman, B. Boggess, J. A. Hermoso, S. Mobashery
Cell-Wall Remodeling By The Zinc-Protease Ampdh3 From Pseudomonas Aeruginosa.
J. Am. Chem. Soc. V. 135 12604 2013
PubMed-ID: 23931161  |  Reference-DOI: 10.1021/JA407445X

(-) Compounds

Molecule 1 - AMPDH3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA PAO1
    Organism Taxid: 208964
 
Molecule 2 - PEPTIDE
    Chains: C, D
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric Unit (6, 14)
No.NameCountTypeFull Name
16CL2Mod. Amino Acid6-CARBOXYLYSINE
2DAL2Mod. Amino AcidD-ALANINE
3FGA2Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
4MAG2Ligand/IonBETA-METHYL-N-ACETYL-D-GLUCOSAMINE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
6ZN2Ligand/IonZINC ION
Biological Unit 1 (5, 12)
No.NameCountTypeFull Name
16CL2Mod. Amino Acid6-CARBOXYLYSINE
2DAL2Mod. Amino AcidD-ALANINE
3FGA2Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
4MAG2Ligand/IonBETA-METHYL-N-ACETYL-D-GLUCOSAMINE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
6ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARE6CL C:3BINDING SITE FOR RESIDUE DAL C 4
2AC2SOFTWAREARG B:76 , ASN B:90 , FGA D:2 , 6CL D:3BINDING SITE FOR RESIDUE DAL D 4
3AC3SOFTWAREHIS A:25 , HIS A:146 , ASP A:156 , HOH A:2005 , ALA C:1BINDING SITE FOR RESIDUE ZN A1260
4AC4SOFTWAREHIS B:25 , HIS B:146 , ASP B:156 , HOH B:2008BINDING SITE FOR RESIDUE ZN B1256
5AC5SOFTWARETYR A:26 , THR A:27 , GLU A:99 , ALA A:104 , ARG A:105 , ASP A:106 , PHE A:111 , ARG A:153 , LYS A:154 , HOH A:2005 , ALA C:1BINDING SITE FOR POLY-SACCHARIDE RESIDUES MAG A1257 THROUGH NAG A1259
6AC6SOFTWARETYR A:26 , THR A:27 , GLU A:99 , ALA A:104 , ARG A:105 , ASP A:106 , PHE A:111 , ARG A:153 , LYS A:154 , HOH A:2005 , TYR B:26 , THR B:27 , LEU B:29 , GLU B:99 , ASP B:106 , PHE B:111 , GLY B:152 , ARG B:153 , LYS B:154 , SER B:155 , HOH B:2008 , HOH B:2009 , ALA C:1 , ALA D:1BINDING SITE FOR POLY-SACCHARIDE RESIDUES MAG B1257 THROUGH NAG B1259

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asp A:108 -Gly A:109
2Asp A:156 -Pro A:157
3Gly B:64 -Gln B:65
4Asp B:108 -Gly B:109
5Val B:151 -Gly B:152
6Asp B:156 -Pro B:157
76cl C:3 -Dal C:4
86cl D:3 -Dal D:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BXD)

(-) 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:255
 aligned with Q9I5D1_PSEAE | Q9I5D1 from UniProtKB/TrEMBL  Length:255

    Alignment length:255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250     
         Q9I5D1_PSEAE     1 MLTIDYNSYRTTTPYGKRVRFLVLHYTALDFAASVKALTTGAASAHYLIPAPHDPSYKAAGFKGQRIFNLVAEEDRAWHAGVSGWARRDNLNDTSIGIEIVNLARDDDGVFTFPDYERSQINALKQLAKNILQRYPDMTPKNVVGHSDIAVGRKSDPGPKLPWKELYEAGIGAWYDDATRDRYREGFERDGLPPRADLLEAFRLYGYALPATVDDAYFASLLRAFQMHFRPENYDGALDVETAAILYALNEKYPA 255
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeee...hhhhhhhhhhh......eee....hhhhhhh.......ee.....eee............hhhh.eeeeee....ee....ee....hhhhhhhhhhhhhhhhh.....hhh.eeehhhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bxd A   1 MLTIDYNSYRTTTPYGKRVRFLVLHYTALDFAASVKALTTGAASAHYLIPAPHDPSYKAAGFKGQRIFNLVAEEDRAWHAGVSGWARRDNLNDTSIGIEIVNLARDDDGVFTFPDYERSQINALKQLAKNILQRYPDMTPKNVVGHSDIAVGRKSDPGPKLPWKELYEAGIGAWYDDATRDRYREGFERDGLPPRADLLEAFRLYGYALPATVDDAYFASLLRAFQMHFRPENYDGALDVETAAILYALNEKYPA 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250     


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with Q9I5D1_PSEAE | Q9I5D1 from UniProtKB/TrEMBL  Length:255

    Alignment length:255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250     
         Q9I5D1_PSEAE     1 MLTIDYNSYRTTTPYGKRVRFLVLHYTALDFAASVKALTTGAASAHYLIPAPHDPSYKAAGFKGQRIFNLVAEEDRAWHAGVSGWARRDNLNDTSIGIEIVNLARDDDGVFTFPDYERSQINALKQLAKNILQRYPDMTPKNVVGHSDIAVGRKSDPGPKLPWKELYEAGIGAWYDDATRDRYREGFERDGLPPRADLLEAFRLYGYALPATVDDAYFASLLRAFQMHFRPENYDGALDVETAAILYALNEKYPA 255
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee...eeeeee...hhhhhhhhhhh......eee....hhhhhhh.......ee.........................eeeeee....eee..eee....hhhhhhhhhhhhhhhhh.....hhh.eeehhhhh...........hhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bxd B   1 MLTIDYNSYRTTTPYGKRVRFLVLHYTALDFAASVKALTTGAASAHYLIPAPHDPSYKAAGFKGQRIFNLVAEEDRAWHAGVSGWARRDNLNDTSIGIEIVNLARDDDGVFTFPDYERSQINALKQLAKNILQRYPDMTPKNVVGHSDIAVGRKSDPGPKLPWKELYEAGIGAWYDDATRDRYREGFERDGLPPRADLLEAFRLYGYALPATVDDAYFASLLRAFQMHFRPENYDGALDVETAAILYALNEKYPA 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250     


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               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
                 4bxd C   1 Axkx   4
                             |||
                             2-FGA
                              3-6CL
                               4-DAL


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               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
                 4bxd D   1 Axkx   4
                             |||
                             |||
                             2-FGA
                              3-6CL
                               4-DAL
   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 4BXD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9I5D1_PSEAE | Q9I5D1)
molecular function
    GO:0008745    N-acetylmuramoyl-L-alanine amidase activity    Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.
    GO:0009254    peptidoglycan turnover    The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
cellular component
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

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    Asp A:108 - Gly A:109   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q9I5D1_PSEAE | Q9I5D1: 4bxe 4bxj

(-) Related Entries Specified in the PDB File

4bxe CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH ANHYDROMURAMIC PENTAPEPTIDE
4bxj CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA