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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-N-ACETYLMURAMATE-ALANINE LIGASE MURC (TM0231) FROM THERMOTOGA MARITIMA AT 2.3 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  29 Aug 02  (Deposition) - 06 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Tm0231, Udp-N-Acetylmuramate-Alanine Ligase Murc, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Spraggon, R. Schwarzenbacher, A. Kreusch, C. C. Lee, P. Abdubek, E. Ambing, T. Biorac, L. S. Brinen, J. M. Canaves, J. Cambell, H. J. Chiu, X. Dai, A. M. Deacon, M. Didonato, M. A. Elsliger, S. Eshagi, R. Floyd, A. Godzik, C. Grittini, S. K. Grzechnik, E. Hampton, L. Jaroszewski, C. Karlak, H. E. Klock, E. Koesema, J. S. Kovarik, P. Kuhn, I. Levin, D. Mcmullan, T. M. Mcphillips, M. D. Miller, A. Morse, K. Moy, J. Ouyang, R. Page, K. Quijano, A. Robb, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, F. Von Delft, X. Wang, B. West, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, S. A. Lesley, I. A. Wilson
Crystal Structure Of An Udp-N-Acetylmuramate-Alanine Ligase Murc (Tm0231) From Thermotoga Maritima At 2. 3 A Resolution.
Proteins V. 55 1078 2004
PubMed-ID: 15146505  |  Reference-DOI: 10.1002/PROT.20034
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMATE-ALANINE LIGASE MURC
    Chains: A
    EC Number: 6.3.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0231
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: UDP-N-ACETYLMURAMOYL-L-ALANINE SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1J6U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J6U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:50 -Pro A:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J6U)

(-) Exons   (0, 0)

(no "Exon" information available for 1J6U)

(-) 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:430
 aligned with MURC_THEMA | Q9WY73 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:447
                             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       329       339       349       359       369       379       389       399       409       419       429       439       
           MURC_THEMA     - -MKIHFVGIGGIGMSAVALHEFSNGNDVYGSNIEETERTAYLRKLGIPIFVPHSADNWYDPDLVIKTPAVRDDNPEIVRARMERVPIENRLHYFRDTLKREKKEEFAVTGTDGKTTTTAMVAHVLKHLRKSPTVFLGGIMDSLEHGNYEKGNGPVVYELDESEEFFSEFSPNYLIITNARGDHLENYGNSLTRYRSAFEKISRNTDLVVTFAEDELTSHLGDVTFGVKKGTYTLEMRSASRAEQKAMVEKNGKRYLELKLKVPGFHNVLNALAVIALFDSLGYDLAPVLEALEEFRGVHRRFSIAFHDPETNIYVIDDYAHTPDEIRNLLQTAKEVFENEKIVVIFQPHRYSRLEREDGNFAKALQLADEVVVTEVYDAFEEKKNGISGKMIWDSLKSLGKEAYFVEKLPELEKVISVSENTVFLFVGAGDIIYSSRRFVERYQSSK 446
               SCOP domains d1j6ua1 A:0-88 UDP-N-acetylmuramate-alanine ligase MurC                                  d1j6ua3 A:89-295 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                                                                      d1j6ua2 A:296-446 UDP-N-acetylmuramate-alanine ligase         MurC                                                                                      SCOP domains
               CATH domains --1j6uA01 A:2-88 NAD(P)-binding Rossmann-like Domain                                     1j6uA02 A:89-297  [code=3.40.1190.10, no name defined]                                                                                                                                                           1j6uA03 A:298-446  [code=3.90.190.20, no name define        d]                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...ee............eeee.......hhhhhhhhhh...eeehhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh....eee............ee.....eeeee...hhhhhhh...eeee......hhhhhh.hhhhhhhhhhhhhhh..eeeee.....hhhhh.eee......eeeeeeee....eeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......eeeeee....eeeeee...hhhhhhhhhhhhhhhh...eeeeee....--------hhhhhhhh...eeee.....---------hhhhhhhhhhhh...eee..hhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j6u A   0 HmKIHFVGIGGIGmSAVALHEFSNGNDVYGSNIEETERTAYLRKLGIPIFVPHSADNWYDPDLVIKTPAVRDDNPEIVRARmERVPIENRLHYFRDTLKREKKEEFAVTGTDGKTTTTAmVAHVLKHLRKSPTVFLGGImDSLEHGNYEKGNGPVVYELDESEEFFSEFSPNYLIITNARGDHLENYGNSLTRYRSAFEKISRNTDLVVTFAEDELTSHLGDVTFGVKKGTYTLEmRSASRAEQKAmVEKNGKRYLELKLKVPGFHNVLNALAVIALFDSLGYDLAPVLEALEEFRGVHRRFSIAFHDPETNIYVIDDYAHTPDEIRNLLQTAKEVFENEKIVVIFQPHR--------GNFAKALQLADEVVVTEVYD---------SGKmIWDSLKSLGKEAYFVEKLPELEKVISVSENTVFLFVGAGDIIYSSRRFVERYQSSK 446
                             |       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       329       339       349       359       369       | -       389|      399       409       419       429       439       
                             |          13-MSE                                                              81-MSE                               119-MSE             139-MSE                                                                                         235-MSE    246-MSE                                                                                                349      358                377       387  |                                                        
                             1-MSE                                                                                                                                                                                                                                                                                                                                                                                              390-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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J6U)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MURC_THEMA | Q9WY73)
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: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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