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(-) Description

Title :  CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA
 
Authors :  C. Carrasco-Lopez, J. A. Hermoso
Date :  12 Jul 13  (Deposition) - 09 Oct 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase (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
    EC Number: 3.5.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET 28
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA PAO1
    Organism Taxid: 208964

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:60 , GLY A:61 , PHE A:62 , GOL A:1257 , HOH A:2148BINDING SITE FOR RESIDUE GOL A1256
2AC2SOFTWAREGOL A:1256 , HOH A:2150BINDING SITE FOR RESIDUE GOL A1257
3AC3SOFTWARETYR A:26 , ALA A:28 , ASP A:106 , PHE A:111BINDING SITE FOR RESIDUE GOL A1258

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asp A:156 -Pro A:157
2Arg B:105 -Asp B:106
3Val B:151 -Gly B:152
4Asp B:156 -Pro B:157
5Glu B:185 -Gly B:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BXJ)

(-) 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:254
 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 ...ee.........eee...eeeeee...hhhhhhhhhhh......eee....hhhhhhh......eee.....eee......ee..ee.....eeeeee....ee..-.ee....hhhhhhhhhhhhhhhhh.....hhh.eeehhhhh...........hhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bxj A   1 MLTIDYNSYRTTTPYGKRVRFLVLHYTALDFAASVKALTTGAASAHYLIPAPHDPSYKAAGFKGQRIFNLVAEEDRAWHAGVSGWARRDNLNDTSIGIEIVNLARDDD-VFTFPDYERSQINALKQLAKNILQRYPDMTPKNVVGHSDIAVGRKSDPGPKLPWKELYEAGIGAWYDDATRDRYREGFERDGLPPRADLLEAFRLYGYALPATVDDAYFASLLRAFQMHFRPENYDGALDVETAAILYALNEKYPA 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     
                                                                                                                                     108 |                                                                                                                                                 
                                                                                                                                       110                                                                                                                                                 


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 ...ee.........eee...eeeeee...hhhhhhhhhhhh.....eee....hhhhhhh......eee.....eee......ee..ee.....eeeeee....ee....ee....hhhhhhhhhhhhhhhhh.....hhh.eeehhhhh...........hhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bxj 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
   Legend:   → Mismatch (orange background)
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  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 4BXJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        Q9I5D1_PSEAE | Q9I5D1: 4bxd 4bxe

(-) Related Entries Specified in the PDB File

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