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(-) Description

Title :  CRYSTAL STRUCTURE OF MURF LIGASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH ADP
 
Authors :  S. Favini-Stabile, C. Contreras-Martel, N. Thielens, A. Dessen
Date :  29 Jan 13  (Deposition) - 11 Sep 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Peptidoglycan Synthesis, Adp-Forming Enzyme, Cell Wall, Cell Shape, Cell Cycle, Nucleotide-Binding, Atp-Binding, Cell Division (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Favini-Stabile, C. Contreras-Martel, N. Thielens, A. Dessen
Mreb And Murg As Scaffolds For The Cytoplasmic Steps Of Peptidoglycan Biosynthesis
Environ. Microbiol. V. 15 3218 2013
PubMed-ID: 23826965  |  Reference-DOI: 10.1111/1462-2920.12171

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
    Chains: A
    EC Number: 6.3.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: MURF LIGASE

 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
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:325 , ASP A:359 , LYS A:377 , HOH A:2167BINDING SITE FOR RESIDUE GOL A1000
2AC2SOFTWARESER A:90 , SER A:91 , GLY A:92 , LYS A:93 , THR A:94 , THR A:95 , ASN A:258 , GLY A:260 , ASN A:264 , ARG A:293 , PHE A:294 , ASP A:307 , ASN A:310 , LYS A:405 , HOH A:2065 , HOH A:2070 , HOH A:2071 , HOH A:2119 , HOH A:2120 , HOH A:2181BINDING SITE FOR RESIDUE ADP A1441

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZL8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZL8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZL8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZL8)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZL8)

(-) 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:427
 aligned with Q9WY78_THEMA | Q9WY78 from UniProtKB/TrEMBL  Length:426

    Alignment length:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   426 
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420     | 
         Q9WY78_THEMA     1 MKDLLTRRFVLNSKEVREGDVFVAVKGKRFDGHDFIDEALRNGAYAIIAERKTVNSDRIFLVESSVDTLAKLAREKLGNFSGTVVGVTGSSGKTTTKEILYNLLKNKRSVFKTPGNMNTEYGLPLSILNDYKGEEILVLEMAASRPGDIAHLCKIAPPDVAVLLNVGSAHLEFFGTRERIMETKMEIIKHSKENAIAVTLFDDPDLRKEVPRYRNTLFFGKEGGDSVLKDWWYYEGSTIAEFEAFDSLFTVKLSGYWNGGQLLNIAASLCVMRTLGETVDIFDLASLKTVPGRFNVREKKGVLIVDDTYNASPEAFQTSIEALLRFPGKKFAVVGAMKELGERSKEFHEELGERLNVLDGVYVFLSEPEAEWIKSKKIILKSDDPEKIAKDLATRVKKGDVVLFKASRAVRIERVLEMFEKELEKR-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.ee.hhhhh....eee........hhhhhhhhhhh...eeee.........eee..hhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhh....eee........hhhhhhhhhhh....eeeee......hhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhh.eeeeee.....eeeeeeeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhh....hhhhhhh........eeeee..eeeeee....hhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh...eeeee..hhhhhhh....eeeee.hhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zl8 A   1 MKDLLTRRFVLNSKEVREGDVFVAVKGKRFDGHDFIDEALRNGAYAIIAERKTVNSDRIFLVESSVDTLAKLAREKLGNFSGTVVGVTGSSGKTTTKEILYNLLKNKRSVFKTPGNMNTEYGLPLSILNDYKGEEILVLEMAASRPGDIAHLCKIAPPDVAVLLNVGSAHLEFFGTRERIMETKMEIIKHSKENAIAVTLFDDPDLRKEVPRYRNTLFFGKEGGDSVLKDWWYYEGSTIAEFEAFDSLFTVKLSGYWNGGQLLNIAASLCVMRTLGETVDIFDLASLKTVPGRFNVREKKGVLIVDDTYNASPEAFQTSIEALLRFPGKKFAVVGAMKELGERSKEFHEELGERLNVLDGVYVFLSEPEAEWIKSKKIILKSDDPEKIAKDLATRVKKGDVVLFKASRAVRIERVLEMFEKELEKRA 427
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
   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 3ZL8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZL8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZL8)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9WY78_THEMA | Q9WY78)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0047480    UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity    Catalysis of the reaction: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine + ATP + D-alanyl-D-alanine = phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + ADP.
    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: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.
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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