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(-) Description

Title :  MURC - CRYSTAL STRUCTURE OF THE ENZYME FROM HAEMOPHILUS INFLUENZAE COMPLEXED WITH AMPPCP
 
Authors :  T. Skarzynski, A. Cleasby, E. Domenici, M. Gevi, J. Shaw
Date :  06 Dec 01  (Deposition) - 13 Jun 03  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Wall Biosynthesis, Peptidoglycan, Murein, Ligase, Atp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Skarzynski, A. Cleasby, E. Domenici, M. Gevi, J. Shaw
Crystal Structures Of Udp-N-Acetylmuramate-L-Alanine Ligase (Murc) From Haemophilus Influenzae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMATE-L-ALANINE LIGASE
    Chains: A, B
    EC Number: 6.3.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21
    Expression System Taxid: 562
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:130 , GLU A:173 , ACP A:1476 , HOH A:2125BINDING SITE FOR RESIDUE MG A1477
2AC2SOFTWARETHR B:130 , GLU B:173 , ACP B:1475 , HOH B:2195BINDING SITE FOR RESIDUE MG B1476
3AC3SOFTWARETHR A:126 , HIS A:127 , GLY A:128 , LYS A:129 , THR A:130 , THR A:131 , GLU A:173 , ASN A:193 , HIS A:291 , ASN A:295 , ARG A:326 , ASP A:345 , TYR A:346 , GLY A:347 , HIS A:348 , GLU A:352 , VAL A:355 , THR A:356 , MG A:1477 , HOH A:2297 , HOH A:2410 , HOH A:2411 , HOH A:2412 , HOH A:2413BINDING SITE FOR RESIDUE ACP A1476
4AC4SOFTWARETHR B:126 , HIS B:127 , GLY B:128 , LYS B:129 , THR B:130 , THR B:131 , GLU B:173 , ASN B:193 , HIS B:291 , ASN B:295 , ARG B:326 , ASP B:345 , TYR B:346 , GLY B:347 , HIS B:348 , GLU B:352 , THR B:356 , MG B:1476 , HOH B:2401 , HOH B:2407 , HOH B:2510 , HOH B:2511 , HOH B:2512BINDING SITE FOR RESIDUE ACP B1475

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GQY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GQY)

(-) 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:468
 aligned with MURC_HAEIN | P45066 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:475
                                    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       430       440       450       460       470     
           MURC_HAEIN     1 MKHSHEEIRKIIPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESWKN 475
               SCOP domains d1gqya1 A:1-106 UDP-N-acetylmuramate-alanine ligase MurC                                                  d1gqya3 A:107-321 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                                                                             d1gqya2 A:322-475 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                 SCOP domains
               CATH domains ------------------1gqyA01 A:19-106 NAD(P)-binding Rossmann-like Domain                                    1gqyA02 A:107-323  [code=3.40.1190.10, no name defined]                                                                                                                                                                  1gqyA03 A:324-475  [code=3.90.190.20, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh........eeeee.....hhhhhhhhhhhhh.eeeeee...hhhhhhhhhhh.eeee..hhhhhh...eeee.......hhhhhhhhhh...eeehhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh....eee...........ee.....eeeee..hhhhhhhhh...eeee......-------hhhhhhhhhhhhhhh.....eeeee..hhhhhhhh.....eeeeee......eeeeeeeee..eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhh....eee.hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gqy A   1 MKHSHEEIRKIIPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPD-------DFEKMKATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESWKN 475
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      |  -    |  210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470     
                                                                                                                                                                                                                              197     205                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:469
 aligned with MURC_HAEIN | P45066 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:469
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465         
           MURC_HAEIN     6 EEIRKIIPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESWK 474
               SCOP domains d1gqyb1 B:6-106 UDP-N-acetylmuramate-alanine ligase MurC                                             d1gqyb3 B:107-321 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                                                                             d1gqyb2 B:322-474 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                SCOP domains
               CATH domains -------------1gqyB01 B:19-106 NAD(P)-binding Rossmann-like Domain                                    1gqyB02 B:107-323  [code=3.40.1190.10, no name defined]                                                                                                                                                                  1gqyB03 B:324-474  [code=3.90.190.20, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh........eeeee.....hhhhhhhhhhhhh.eeeeee...hhhhhhhhhhh.eeee..hhhhhh...eeee.......hhhhhhhhhh...eeehhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh....eee...........ee.....eeeee..hhhhhhhhh...eeee.............hhhhhhhhhhhhhhh.....eeeee..hhhhhhhh.....eeeeee......eeeeeeeee..eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhh....eee.hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gqy B   6 EEIRKIIPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESWK 474
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465
   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  (3, 6)

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

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MURC_HAEIN | P45066)
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MURC_HAEIN | P45066: 1gqq 1p31 1p3d

(-) Related Entries Specified in the PDB File

1gqq MURC - CRYSTAL STRUCTURE OF THE APO-ENZYME FROM HAEMOPHILUS INFLUENZAE