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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-N-ACETYLMURAMIC ACID:L-ALANINE LIGASE (MURC) IN COMPLEX WITH UMA AND ANP.
 
Authors :  C. D. Mol, A. Brooun, D. R. Dougan, M. T. Hilgers, L. W. Tari, R. A. Wijnands, M. W. Knuth, D. E. Mcree, R. V. Swanson
Date :  17 Apr 03  (Deposition) - 15 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta Protein, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Mol, A. Brooun, D. R. Dougan, M. T. Hilgers, L. W. Tari, R. A. Wijnands, M. W. Knuth, D. E. Mcree, R. V. Swanson
Crystal Structures Of Active Fully Assembled Substrate- And Product-Bound Complexes Of Udp-N-Acetylmuramic Acid:L-Alanine Ligase (Murc) From Haemophilus Influenzae.
J. Bacteriol. V. 185 4152 2003
PubMed-ID: 12837790  |  Reference-DOI: 10.1128/JB.185.14.4152-4162.2003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMATE--ALANINE LIGASE
    Chains: A, B
    EC Number: 6.3.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSX29
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MURC
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: UDP-N-ACETYLMURAMOYL-L-ALANINE SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 36)

Asymmetric Unit (4, 36)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MN4Ligand/IonMANGANESE (II) ION
3MSE28Mod. Amino AcidSELENOMETHIONINE
4UMA2Ligand/IonURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MN-1Ligand/IonMANGANESE (II) ION
3MSE14Mod. Amino AcidSELENOMETHIONINE
4UMA1Ligand/IonURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MN-1Ligand/IonMANGANESE (II) ION
3MSE14Mod. Amino AcidSELENOMETHIONINE
4UMA1Ligand/IonURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:198 , ANP A:603 , HOH A:978 , HOH A:979 , HOH A:980 , HOH A:981BINDING SITE FOR RESIDUE MN A 604
2AC2SOFTWARETHR A:130 , GLU A:173 , ANP A:603 , HOH A:983 , HOH A:984BINDING SITE FOR RESIDUE MN A 605
3AC3SOFTWAREHIS B:198 , HOH B:972 , HOH B:973 , HOH B:974 , UMA B:1602 , ANP B:1603BINDING SITE FOR RESIDUE MN B 1604
4AC4SOFTWARETHR B:130 , GLU B:173 , HOH B:976 , HOH B:977 , ANP B:1603BINDING SITE FOR RESIDUE MN B 1605
5AC5SOFTWAREGLY A:25 , GLY A:27 , GLY A:28 , ALA A:29 , GLY A:30 , MSE A:31 , ASP A:49 , ILE A:50 , HIS A:70 , SER A:84 , SER A:85 , ALA A:86 , ILE A:87 , ARG A:107 , ASP A:175 , TYR A:346 , HIS A:348 , HIS A:376 , ARG A:377 , ARG A:380 , HOH A:606 , HOH A:635 , HOH A:730 , HOH A:763 , HOH A:779 , HOH A:887 , HOH A:906 , HOH A:984 , HOH A:1021 , HOH A:1048 , HOH A:1082 , HOH A:1095 , HOH A:1165 , HOH A:1319 , HOH A:1392 , HOH A:1415 , HOH A:1417BINDING SITE FOR RESIDUE UMA A 602
6AC6SOFTWARETHR A:126 , HIS A:127 , GLY A:128 , LYS A:129 , THR A:130 , THR A:131 , GLU A:173 , 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 , MN A:604 , MN A:605 , HOH A:730 , HOH A:978 , HOH A:979 , HOH A:980 , HOH A:981 , HOH A:982 , HOH A:983 , HOH A:1001 , HOH A:1165BINDING SITE FOR RESIDUE ANP A 603
7AC7SOFTWAREGLY B:25 , GLY B:27 , GLY B:28 , ALA B:29 , GLY B:30 , MSE B:31 , ASP B:49 , ILE B:50 , HIS B:70 , SER B:84 , SER B:85 , ALA B:86 , ILE B:87 , ARG B:107 , GLU B:173 , ASP B:175 , SER B:177 , HIS B:198 , TYR B:346 , HIS B:348 , HIS B:376 , ARG B:377 , ARG B:380 , HOH B:612 , HOH B:621 , HOH B:667 , HOH B:705 , HOH B:850 , HOH B:905 , HOH B:938 , HOH B:977 , HOH B:985 , HOH B:1019 , HOH B:1080 , ANP B:1603 , MN B:1604BINDING SITE FOR RESIDUE UMA B 1602
8AC8SOFTWARETHR 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 , VAL B:355 , THR B:356 , HOH B:850 , HOH B:972 , HOH B:973 , HOH B:974 , HOH B:975 , HOH B:976 , HOH B:977 , HOH B:985 , HOH B:993 , UMA B:1602 , MN B:1604 , MN B:1605BINDING SITE FOR RESIDUE ANP B 1603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P3D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P3D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P3D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P3D)

(-) Exons   (0, 0)

(no "Exon" information available for 1P3D)

(-) Sequences/Alignments

Asymmetric 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:463
 aligned with MURC_HAEIN | P45066 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:463
                                    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    11 IIPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESW 473
               SCOP domains d1p3da1 A:11-106 UDP-N-acetylmuramate-alanine ligase MurC                                       d1p3da3 A:107-321 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                                                                             d1p3da2 A:322-473 UDP-N-acetylmuramate-alanine ligase MurC                                                                                               SCOP domains
               CATH domains --------1p3dA01 A:19-106 NAD(P)-binding Rossmann-like Domain                                    1p3dA02 A:107-323  [code=3.40.1190.10, no name defined]                                                                                                                                                                  1p3dA03 A:324-473  [code=3.90.190.20, no name defined]                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.....hhhhhhhhhhhhh.eeeeee...hhhhhhhhhh..eeee..hhhhhh...eeee.......hhhhhhhhhh...eeehhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh....eee...........ee.....eeeee.....hhhhhh...eeee......hhhhhh.hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhh.eeeeee......eeeeeeeee..eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhh....eee.hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p3d A  11 IIPEmRRVQQIHFIGIGGAGmSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQmLAEImRFRHGIAVAGTHGKTTTTAmISmIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPmVSVVTNmEPDHmDTYEGDFEKmKATYVKFLHNLPFYGLAVmCADDPVLmELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVmIFQPHRYSRTRDLFDDFVQVLSQVDALImLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESW 473
                                |   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   
                                |              31-MSE                                                                        110-MSE|                 135-MSE                                             187-MSE  |    |       209-MSE            228-MSE 236-MSE                                                                                                                                371-MSE                      400-MSE                                                                     
                               15-MSE                                                                                             115-MSE                138-MSE                                                 194-MSE|                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                      199-MSE                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:460
 aligned with MURC_HAEIN | P45066 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:460
                                    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       453       463       473
           MURC_HAEIN    14 EMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESW 473
               SCOP domains d1p3db1 B:14-106 UDP-N-acetylmuramate-alanine ligase MurC                                    d1p3db3 B:107-321 UDP-N-acetylmuramate-alanine ligase MurC                                                                                                                                                             d1p3db2 B:322-473 UDP-N-acetylmuramate-alanine ligase MurC                                                                                               SCOP domains
               CATH domains -----1p3dB01 B:19-106 NAD(P)-binding Rossmann-like Domain                                    1p3dB02 B:107-323  [code=3.40.1190.10, no name defined]                                                                                                                                                                  1p3dB03 B:324-473  [code=3.90.190.20, no name defined]                                                                                                 CATH domains
           Pfam domains (1) ------Mur_ligase-1p3dB01 B:20-119                                                                         ---Mur_ligase_M-1p3dB05 B:123-303                                                                                                                                                       -------------------Mur_ligase_C-1p3dB03 B:323-414                                                              ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------Mur_ligase-1p3dB02 B:20-119                                                                         ---Mur_ligase_M-1p3dB06 B:123-303                                                                                                                                                       -------------------Mur_ligase_C-1p3dB04 B:323-414                                                              ----------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh..eeee..hhhhhh...eeee.......hhhhhhhhhh...eeehhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh....eee...........ee.....eeeee.....hhhhhh...eeee.............hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhh.eeeeee......eeeeeeeee..eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhh......eee.hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p3d B  14 EmRRVQQIHFIGIGGAGmSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQmLAEImRFRHGIAVAGTHGKTTTTAmISmIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPmVSVVTNmEPDHmDTYEGDFEKmKATYVKFLHNLPFYGLAVmCADDPVLmELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVmIFQPHRYSRTRDLFDDFVQVLSQVDALImLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESW 473
                             |      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       453       463       473
                            15-MSE          31-MSE                                                                        110-MSE|                 135-MSE                                             187-MSE  |    |       209-MSE            228-MSE 236-MSE                                                                                                                                371-MSE                      400-MSE                                                                     
                                                                                                                               115-MSE                138-MSE                                                 194-MSE|                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                   199-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  (3, 6)

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

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Mur_ligase_C] (24)
(-)
Clan: no clan defined [family: Mur_ligase_M] (23)

(-) Gene Ontology  (11, 11)

Asymmetric 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 1gqy 1p31

(-) Related Entries Specified in the PDB File

1p31 CRYSTAL STRUCTURE OF UDP-N-ACETYLMURAMIC ACID:L-ALANINE LIGASE (MURC) IN COMPLEX WITH UNAM