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(-) Description

Title :  SOLUTION STRUCTURE OF CITROBACTER FREUNDII AMPD
 
Authors :  E. Liepinsh, C. Genereux, D. Dehareng, B. Joris, G. Otting
Date :  31 Jan 03  (Deposition) - 18 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Mixed Alpha-Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Liepinsh, C. Genereux, D. Dehareng, B. Joris, G. Otting
Nmr Structure Of Citrobacter Freundii Ampd, Comparison With Bacteriophage T7 Lysozyme And Homology With Pgrp Domains
J. Mol. Biol. V. 327 833 2003
PubMed-ID: 12654266  |  Reference-DOI: 10.1016/S0022-2836(03)00185-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMPD PROTEIN
    Chains: A
    EC Number: 3.5.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: CITROBACTER FREUNDII
    Organism Taxid: 546
    Synonym: AMPD

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:34 , HIS A:154 , ASP A:164BINDING SITE FOR RESIDUE ZN A 210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J3G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J3G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J3G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J3G)

(-) Exons   (0, 0)

(no "Exon" information available for 1J3G)

(-) Sequences/Alignments

NMR Structure
   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:187
 aligned with AMPD_CITFR | P82974 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
           AMPD_CITFR     1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVTPSSHKEMT 187
               SCOP domains d1j3ga_ A: AmpD protein                                                                                                                                                                     SCOP domains
               CATH domains 1j3gA00 A:1-187 Lysozyme                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee...ee.................ee..ee........hhhhhhhhhh......hhhhhhhh.......eeee...eeee.............eee..eee........eee........hhhhhhhhhhhhhhhhhh.hhhh.ee.................hhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3g A   1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVTPSSHKEMT 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J3G)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (AMPD_CITFR | P82974)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1j3g
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  AMPD_CITFR | P82974
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPD_CITFR | P82974: 2y28 2y2b 2y2c 2y2d 2y2e

(-) Related Entries Specified in the PDB File

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