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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  A MODEL STRUCTURE OF UDP-N-ACETYLMURAMOYL: L-ALANINE SYNTHETASE (MURC) FROM ESCHERICHIA COLI BASED ON HOMOLOGY AND HYDROPHOBIC CLUSTER ANALYSIS AND ITS VALIDATION BY AMINO ACID MODIFICATIONS.
 
Authors :  F. Nosal, R. Legrand, D. A. Rowlands, P. Ferrari, B. Schoot, J. Van Heijenoort
Date :  04 Mar 99  (Deposition) - 30 Dec 03  (Release) - 30 Dec 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Synthetase, Peptidoglycan Biosynthesis, Udp-Murnac: L- Alanine Ligase, Ec 6. 3. 2. 8 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Nosal, R. Legrand, D. A. Rowlands, P. Ferrari, B. Schoot, J. Van Heijenoort
A Model Structure Of Udp-N-Acetylmuramoyl: L-Alanine Synthetase (Murc) From Escherichia Coli Based On Homology And Hydrophobic Cluster Analysis And Its Validation By Amino Acid Modifications
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    Chains: A
    EC Number: 6.3.2.8
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
    Strain: JM83
    Synonym: MURC

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Theoretical Model (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2UPM1Ligand/IonURIDINE-5'-DIPHOSPHATE-N-1-HYDROOXY-ETHANOYL MURAMAICACID

(-) Sites  (0, 0)

(no "Site" information available for 1CC9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CC9)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Leu A:378 -Phe A:379

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CC9)

(-) Exons   (0, 0)

(no "Exon" information available for 1CC9)

(-) Sequences/Alignments

Theoretical Model
   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:466
 aligned with MURC_ECOLI | P17952 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:466
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477      
           MURC_ECOLI    18 RVRHIHFVGIGGAGMGGIAEVLANEGYQISGSDLAPNPVTQQLMNLGATIYFNHRPENVRDASVVVVSSAISADNPEIVAAHEARIPVIRRAEMLAELMRFRHGIAIAGTHGKTTTTAMVSSIYAEAGLDPTFVNGGLVKAAGVHARLGHGRYLIAEADESDASFLHLQPMVAIVTNIEADHMDTYQGDFENLKQTFINFLHNLPFYGRAVMCVDDPVIRELLPRVGRQTTTYGFSEDADVRVEDYQQIGPQGHFTLLRQDKEPMRVTLNAPGRHNALNAAAAVAVATEEGIDDEAILRALESFQGTGRRFDFLGEFPLEPVNGKSGTAMLVDDYGHHPTEVDATIKAARAGWPDKNLVMLFQPHRFTRTRDLYDDFANVLTQVDTLLMLEVYPAGEAPIPGADSRSLCRTIRGRGKIDPILVPDPARVAEMLAPVLTGNDLILVQGAGNIGKIARSLAEIKLKPQ 483
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee....hhhh.hhhhh.................hhhh................hhhhhhhhh...eee.............eee..hhhhhhh......eeee....hhhhhhhhhhhhhh.................hhh........eee..............eeee.............hhhhhhhhhhh......eeeee...............eeee............................................hhhhhhhhhhhhhhhhh...hhhh............................................hhhhhhhh.........................hhhhh.........................hhhhhhh...........hhhhhhhhh.....................hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cc9 A  18 RVRHIHFVGIGGAGMGGIAEVLANEGYQISGSDLAPNPVTQQLMNLGATIYFNHRPENVRDASVVVVSSAISADNPEIVAAHEARIPVIRRAEMLAELMRFRHGIAIAGTHGKTTTTAMVSSIYAEAGLDPTFVNGGLVKAAGVHARLGHGRYLIAEADESDASFLHLQPMVAIVTNIEADHMDTYQGDFENLKQTFINFLHNLPFYGRAVMCVDDPVIRELLPRVGRQTTTYGFSEDADVRVEDYQQIGPQGHFTLLRQDKEPMRVTLNAPGRHNALNAAAAVAVATEEGIDDEAILRALESFQGTGRRFDFLGEFPLEPVNGKSGTAMLVDDYGHHPTEVDATIKAARAGWPDKNLVMLFQPHRFTRTRDLYDDFANVLTQVDTLLMLEVYPAGEAPIPGADSRSLCRTIRGRGKIDPILVPDPARVAEMLAPVLTGNDLILVQGAGNIGKIARSLAEIKLKPQ 483
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477
   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 1CC9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1CC9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CC9)

(-) Gene Ontology  (13, 13)

Theoretical Model(hide GO term definitions)
Chain A   (MURC_ECOLI | P17952)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008763    UDP-N-acetylmuramate-L-alanine ligase activity    Catalysis of the reaction: L-alanine + ATP + UDP-N-acetylmuramate = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanine.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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: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:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        MURC_ECOLI | P17952: 2f00

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