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(-) Description

Title :  THE CRYSTAL STRUCTURE OF UDP-N-ACETYLMURAMATE:L-ALANYL-GAMMA-D-GLUTAMYL-MESO-DIAMINOPIMELATE LIGASE (MPL) FROM NEISSERIA MENINGITIDES
 
Authors :  C. Chang, R. Hendricks, S. Clancy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  25 Aug 08  (Deposition) - 09 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Neisseria Meningitidis Mc58, Udp-N-Acetylmuramate:L-Alanyl-Gamma-D- Glutamyl-Meso-Diaminopimelate Ligase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Atp-Binding, Ligase, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, R. Hendricks, S. Clancy, A. Joachimiak
The Crystal Structure Of Udp-N-Acetylmuramate:L-Alanyl-Gamma-D-Glutamyl-Meso- Diaminopimelate Ligase (Mpl) From Neisseria Meningitides
To Be Published
PubMed: search

(-) Compounds

Molecule 1
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3) DERIVATIVE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MPL-2, MPL-1, NMB1145, NMB1183
    Organism Scientific: NEISSERIA MENINGITIDIS MC58
    Organism Taxid: 122586

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:89 , TYR A:90 , ILE A:91 , GLN A:95 , HOH A:427 , HIS B:103 , ARG B:188BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWAREGLU A:99 , HIS A:103 , ARG A:188 , PRO B:89 , TYR B:90BINDING SITE FOR RESIDUE GOL B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:37 -Pro A:38
2Pro B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EAG)

(-) 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:324
 aligned with Q9JRY9_NEIMB | Q9JRY9 from UniProtKB/TrEMBL  Length:458

    Alignment length:324
                             1                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319    
         Q9JRY9_NEIMB     - -MKHIHIIGIGGTFMGGLAAIAKEAGFEVSGCDAKMYPPMSTQLEALGIDVYEGFDAAQLDEFKADVYVIGNVAKRGMDVVEAILNLGLPYISGPQWLSENVLHHHWVLGVAGTHGKTTTASMLAWVLEYAGLAPGFLIGGVPENFGVSARLPQTPRQDPNSQSPFFVIEADEYDTAFFDKRSKFVHYRPRTAVLNNLEFDHADIFADLGAIQTQFHYLVRTVPSEGLIVCNGRQQSLQDTLDKGCWTPVEKFGTEHGWQAGEANADGSFDVLLDGKTAGRVKWDLMGRHNRMNALAVIAAARHVGVDIQTACEALGAFKNVKR 323
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3eagA01 A:0-92 NAD(P)-binding Rossmann-like Domain                                           3eagA02 A:93-323  [code=3.40.1190.10, no name defined]                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhh..eeee..hhhhhhh....eeee....................eeehhhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhh....eee...ee......ee..............eeeee....eee..eeee.hhhh...eeee............hhhhhhhhhhhhhh......eeeee..hhhhhhhhh......eeee.....eeeeee.....eeeee..eeeeee.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eag A   0 AmKHIHIIGIGGTFmGGLAAIAKEAGFEVSGCDAKmYPPmSTQLEALGIDVYEGFDAAQLDEFKADVYVIGNVAKRGmDVVEAILNLGLPYISGPQWLSENVLHHHWVLGVAGTHGKTTTASmLAWVLEYAGLAPGFLIGGVPENFGVSARLPQTPRQDPNSQSPFFVIEADEYDTAFFDKRSKFVHYRPRTAVLNNLEFDHADIFADLGAIQTQFHYLVRTVPSEGLIVCNGRQQSLQDTLDKGCWTPVEKFGTEHGWQAGEANADGSFDVLLDGKTAGRVKWDLmGRHNRmNALAVIAAARHVGVDIQTACEALGAFKNVKR 323
                             |       9    |   19        29     |  39        49        59        69       |79        89        99       109       119  |    129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279      |289  |    299       309       319    
                             |           14-MSE               35-MSE                                    77-MSE                                      122-MSE                                                                                                                                                             286-MSE |                               
                             1-MSE                                39-MSE                                                                                                                                                                                                                                                      292-MSE                           


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with Q9JRY9_NEIMB | Q9JRY9 from UniProtKB/TrEMBL  Length:458

    Alignment length:324
                             1                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319    
         Q9JRY9_NEIMB     - -MKHIHIIGIGGTFMGGLAAIAKEAGFEVSGCDAKMYPPMSTQLEALGIDVYEGFDAAQLDEFKADVYVIGNVAKRGMDVVEAILNLGLPYISGPQWLSENVLHHHWVLGVAGTHGKTTTASMLAWVLEYAGLAPGFLIGGVPENFGVSARLPQTPRQDPNSQSPFFVIEADEYDTAFFDKRSKFVHYRPRTAVLNNLEFDHADIFADLGAIQTQFHYLVRTVPSEGLIVCNGRQQSLQDTLDKGCWTPVEKFGTEHGWQAGEANADGSFDVLLDGKTAGRVKWDLMGRHNRMNALAVIAAARHVGVDIQTACEALGAFKNVKR 323
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3eagB01 B:0-92 NAD(P)-binding Rossmann-like Domain                                           3eagB02 B:93-323  [code=3.40.1190.10, no name defined]                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhh....eee....hhhhhh...eeee....................eeehhhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhh....eee...........ee..............eeeee....eee..eeee.hhhh...eeee.............hhhhhhhhhhhhh......eeeee..hhhhhhhhhh.....eeee.....eee........eeeee..eeeeee.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eag B   0 AmKHIHIIGIGGTFmGGLAAIAKEAGFEVSGCDAKmYPPmSTQLEALGIDVYEGFDAAQLDEFKADVYVIGNVAKRGmDVVEAILNLGLPYISGPQWLSENVLHHHWVLGVAGTHGKTTTASmLAWVLEYAGLAPGFLIGGVPENFGVSARLPQTPRQDPNSQSPFFVIEADEYDTAFFDKRSKFVHYRPRTAVLNNLEFDHADIFADLGAIQTQFHYLVRTVPSEGLIVCNGRQQSLQDTLDKGCWTPVEKFGTEHGWQAGEANADGSFDVLLDGKTAGRVKWDLmGRHNRmNALAVIAAARHVGVDIQTACEALGAFKNVKR 323
                             |       9    |   19        29     |  39        49        59        69       |79        89        99       109       119  |    129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279      |289  |    299       309       319    
                             1-MSE       14-MSE               35-MSE                                    77-MSE                                      122-MSE                                                                                                                                                             286-MSE |                               
                                                                  39-MSE                                                                                                                                                                                                                                                      292-MSE
   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 3EAG)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9JRY9_NEIMB | Q9JRY9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016881    acid-amino acid ligase activity    Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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:0009254    peptidoglycan turnover    The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.

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