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(-) Description

Title :  THE CRYSTAL STRUCTURE OF UDP-N-ACETYLMURAMOYLALANINE-D-GLUTAMATE (MURD) LIGASE FROM STREPTOCOCCUS AGALACTIAE TO 1.5A
 
Authors :  A. J. Stein, A. Sather, G. Shakelford, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  27 Jan 10  (Deposition) - 09 Feb 10  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Udp-N-Acetylmuramoylalanine, D-Glutamate, Streptococcus, Agalacitae, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative, Atp- Binding, Cell Cycle, Cell Division, Cell Shape, Cell Wall Biogenesis/Degradation, Cytoplasm, Nucleotide-Binding, Peptidoglycan Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, A. Sather, G. Shakelford, A. Joachimiak
The Crystal Structure Of Udp-N-Acetylmuramoylalanine-D-Glutamate (Murd) Ligase From Streptococcus Agalactiae To 1. 5A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
    Chains: A
    EC Number: 6.3.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MURD, SAG0475
    Organism Scientific: STREPTOCOCCUS AGALACTIAE
    Organism Taxid: 216466
    Strain: 2603V, SEROGROUP V
    Synonym: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE, D-GLUTAMIC ACID-ADDING ENZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:121 , GLY A:122 , LYS A:123 , THR A:124 , HOH A:458 , HOH A:521 , HOH A:549 , HOH A:626 , HOH A:694 , HOH A:829BINDING SITE FOR RESIDUE SO4 A 452
2AC2SOFTWAREGLY A:40 , HIS A:64 , SER A:296 , ASN A:297 , GLN A:298 , HOH A:540 , HOH A:717 , HOH A:734 , HOH A:751 , HOH A:778BINDING SITE FOR RESIDUE SO4 A 453
3AC3SOFTWAREARG A:19 , TRP A:428 , ASN A:433 , PHE A:434BINDING SITE FOR RESIDUE CL A 454

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LK7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LK7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LK7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LK7)

(-) Exons   (0, 0)

(no "Exon" information available for 3LK7)

(-) 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:448
 aligned with MURD_STRA5 | Q8E186 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:448
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443        
           MURD_STRA5     4 ITTFENKKVLVLGLARSGEAAARLLAKLGAIVTVNDGKPFDENPTAQSLLEEGIKVVCGSHPLELLDEDFCYMIKNPGIPYNNPMVKKALEKQIPVLTEVELAYLVSESQLIGITGSNGKTTTTTMIAEVLNAGGQRGLLAGNIGFPASEVVQAANDKDTLVMELSSFQLMGVKEFRPHIAVITNLMPTHLDYHGSFEDYVAAKWNIQNQMSSSDFLVLNFNQGISKELAKTTKATIVPFSTTEKVDGAYVQDKQLFYKGENIMSVDDIGVPGSHNVENALATIAVAKLAGISNQVIRETLSNFGGVKHRLQSLGKVHGISFYNDSKSTNILATQKALSGFDNTKVILIAGGLDRGNEFDELIPDITGLKHMVVLGESASRVKRAAQKAGVTYSDALDVRDAVHKAYEVAQQGDVILLSPANASWDMYKNFEVRGDEFIDTFESLRGE 451
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------Mur_ligase_M-3lk7A02 A:117-290                                                                                                                                                -------------------Mur_ligase_C-3lk7A01 A:310-392                                                     ----------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....hhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh..eeee...hhhhhhh.eeeeee.......hhhhhhhhhh...eehhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhh.......eeeee.hhhhhh........eeee......hhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhh....eeeeee.......eeee..eeee..eeeee.hhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeeee..eeeee.....hhhhhhhhhhhhhhh.eeeee........hhhhhhhhh...eeee...hhhhhhhhhhhh...eee..hhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lk7 A   4 ITTFENKKVLVLGLARSGEAAARLLAKLGAIVTVNDGKPFDENPTAQSLLEEGIKVVCGSHPLELLDEDFCYmIKNPGIPYNNPmVKKALEKQIPVLTEVELAYLVSESQLIGITGSNGKTTTTTmIAEVLNAGGQRGLLAGNIGFPASEVVQAANDKDTLVmELSSFQLmGVKEFRPHIAVITNLmPTHLDYHGSFEDYVAAKWNIQNQmSSSDFLVLNFNQGISKELAKTTKATIVPFSTTEKVDGAYVQDKQLFYKGENImSVDDIGVPGSHNVENALATIAVAKLAGISNQVIRETLSNFGGVKHRLQSLGKVHGISFYNDSKSTNILATQKALSGFDNTKVILIAGGLDRGNEFDELIPDITGLKHmVVLGESASRVKRAAQKAGVTYSDALDVRDAVHKAYEVAQQGDVILLSPANASWDmYKNFEVRGDEFIDTFESLRGE 451
                                    13        23        33        43        53        63        73  |     83    |   93       103       113       123     | 133       143       153       163  |    173|      183      |193       203       213|      223       233       243       253       263   |   273       283       293       303       313       323       333       343       353       363       373 |     383       393       403       413       423      |433       443        
                                                                                                   76-MSE      88-MSE                                  129-MSE                              166-MSE 174-MSE         190-MSE                 214-MSE                                              267-MSE                                                                                                     375-MSE                                                430-MSE
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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 3LK7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LK7)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Mur_ligase_C] (24)
(-)
Clan: no clan defined [family: Mur_ligase_M] (23)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MURD_STRA5 | Q8E186)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008764    UDP-N-acetylmuramoylalanine-D-glutamate ligase activity    Catalysis of the reaction: D-glutamate + ATP + UDP-N-acetylmuramoyl-L-alanine = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate.
    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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