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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI MUR B BOUND TO A NAPHTHYL TETRONIC ACID INIHIBITOR
 
Authors :  R. Chopra, J. Bard, K. Svenson, T. Mansour
Date :  08 Jun 07  (Deposition) - 26 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Mansour, C. E. Caulfield, B. Rasmussen, R. Chopra, G. Krishnamurthy, K. M. Morris, K. Svenson, J. Bard, C. Smeltzer, S. Naughton, S. Antane, Y. Yang, A. Severin, D. Quagliato, P. J. Petersen, G. Singh
Crystal Structure Of E. Coli Mur B Bound To A Napthyl Tetronic Acid Inhibitor
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE
    ChainsA
    EC Number1.1.1.158
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymUDP-N- ACETYLMURAMATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
19731Ligand/Ion(5Z)-3-(4-CHLOROPHENYL)-4-HYDROXY-5-(1-NAPHTHYLMETHYLENE)FURAN-2(5H)-ONE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:190 , LEU A:218 , GLY A:228 , SER A:229 , ASN A:233 , PRO A:252 , TYR A:254 , LYS A:262 , GLN A:288 , LEU A:290 , VAL A:291 , FAD A:402BINDING SITE FOR RESIDUE 973 A 401
2AC2SOFTWAREILE A:45 , LEU A:46 , GLY A:47 , GLU A:48 , GLY A:49 , SER A:50 , ASN A:51 , VAL A:52 , ASN A:65 , ILE A:110 , PRO A:111 , GLY A:112 , CYS A:113 , SER A:116 , ILE A:119 , ILE A:122 , GLY A:123 , ARG A:159 , ALA A:172 , ILE A:173 , ARG A:214 , ASN A:226 , ALA A:227 , GLY A:228 , ARG A:327 , GLU A:334 , 973 A:401 , HOH A:481 , HOH A:500 , HOH A:529BINDING SITE FOR RESIDUE FAD A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q85)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q85)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q85)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.MURB_ECOLI13-183  1A:13-183

(-) Exons   (0, 0)

(no "Exon" information available for 2Q85)

(-) Sequences/Alignments

Asymmetric/Biological 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:341
 aligned with MURB_ECOLI | P08373 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 
           MURB_ECOLI     2 NHSLKPWNTFGIDHNAQHIVCAEDEQQLLNAWQYATAEGQPVLILGEGSNVLFLEDYRGTVIINRIKGIEIHDEPDAWYLHVGAGENWHRLVKYTLQEGMPGLENLALIPGCVGSSPIQNIGAYGVELQRVCAYVDSVELATGKQVRLTAKECRFGYRDSIFKHEYQDRFAIVAVGLRLPKEWQPVLTYGDLTRLDPTTVTPQQVFNAVCHMRTTKLPDPKVNGNAGSFFKNPVVSAETAKALLSQFPTAPNYPQADGSVKLAAGWLIDQCQLKGMQIGGAAVHRQQALVLINEDNAKSEDVVQLAHHVRQKVGEKFNVWLEPEVRFIGASGEVSAVETIS 342
               SCOP domains d2q85a1 A:2-200 Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain                                                                                                   d2q85a2 A:201-342 Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain                                          SCOP domains
               CATH domains 2q85A01 A:2-68                                                     2q85A02 A:69-218  [code=3.30.465.10, no name defined]                                                                                                 2q85A03 A:219-342 Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 1                                       CATH domains
               Pfam domains ---------------FAD_binding_4-2q85A01 A:17-150                                                                                                        ----------------------------------------------------MurB_C-2q85A02 A:203-330                                                                                                        ------------ Pfam domains
         Sec.struct. author .ee.hhhh......eeeeeeee.hhhhhhhhhhhhhhh...eeee.....eee...eeeeeeee....eeeeee..eeeeeee...hhhhhhhhhhhh....hhhhh....hhhhh.....ee..ee....eeeeeeee.....eeeee..........hhhhh.....eeeeeeeeeee........hhhhhhh.....hhhhhhhhhhhhhhhhh......ee........eehhhhhhhhhhhh....eee.....eeehhhhhhhhh.....ee..eee.......eee....hhhhhhhhhhhhhhhhhhhhh.......eee....eehhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------FAD_PCMH  PDB: A:13-183 UniProt: 13-183                                                                                                                                    --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q85 A   2 NHSLKPWNTFGIDHNAQHIVCAEDEQQLLNAWQYATAEGQPVLILGEGSNVLFLEDYRGTVIINRIKGIEIHDEPDAWYLHVGAGENWHRLVKYTLQEGMPGLENLALIPGCVGSSPIQNIGAYGVELQRVCAYVDSVELATGKQVRLTAKECRFGYRDSIFKHEYQDRFAIVAVGLRLPKEWQPVLTYGDLTRLDPTTVTPQQVFNAVCHMRTTKLPDPKVNGNAGSFFKNPVVSAETAKALLSQFPTAPNYPQADGSVKLAAGWLIDQCQLKGMQIGGAAVHRQQALVLINEDNAKSEDVVQLAHHVRQKVGEKFNVWLEPEVRFIGASGEVSAVETIS 342
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 

   Legend:   → Mismatch (orange background)
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    → 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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: FAD_PCMH (53)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MURB_ECOLI | P08373)
molecular function
    GO:0008762    UDP-N-acetylmuramate dehydrogenase activity    Catalysis of the reaction: UDP-N-acetylmuramate + NADP+ = UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine + NADPH + H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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        MURB_ECOLI | P083731mbb 1mbt 1uxy 2mbr

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