ID B4D201_9BACT Unreviewed; 1084 AA.
AC B4D201;
DT 23-SEP-2008, integrated into UniProtKB/TrEMBL.
DT 23-SEP-2008, sequence version 1.
DT 24-JAN-2024, entry version 85.
DE RecName: Full=UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase {ECO:0000256|HAMAP-Rule:MF_00208};
DE EC=6.3.2.13 {ECO:0000256|HAMAP-Rule:MF_00208};
DE AltName: Full=Meso-A2pm-adding enzyme {ECO:0000256|HAMAP-Rule:MF_00208};
DE AltName: Full=Meso-diaminopimelate-adding enzyme {ECO:0000256|HAMAP-Rule:MF_00208};
DE AltName: Full=UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelate ligase {ECO:0000256|HAMAP-Rule:MF_00208};
DE AltName: Full=UDP-MurNAc-tripeptide synthetase {ECO:0000256|HAMAP-Rule:MF_00208};
DE AltName: Full=UDP-N-acetylmuramyl-tripeptide synthetase {ECO:0000256|HAMAP-Rule:MF_00208};
DE Flags: Precursor;
GN Name=murE {ECO:0000256|HAMAP-Rule:MF_00208};
GN ORFNames=CfE428DRAFT_2939 {ECO:0000313|EMBL:EDY19763.1};
OS Chthoniobacter flavus Ellin428.
OC Bacteria; Verrucomicrobiota; Spartobacteria; Chthoniobacterales;
OC Chthoniobacteraceae; Chthoniobacter.
OX NCBI_TaxID=497964 {ECO:0000313|EMBL:EDY19763.1, ECO:0000313|Proteomes:UP000005824};
RN [1] {ECO:0000313|EMBL:EDY19763.1, ECO:0000313|Proteomes:UP000005824}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Ellin428 {ECO:0000313|EMBL:EDY19763.1,
RC ECO:0000313|Proteomes:UP000005824};
RX PubMed=21460085; DOI=10.1128/JB.00295-11;
RA Kant R., van Passel M.W., Palva A., Lucas S., Lapidus A.,
RA Glavina Del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S.,
RA Larimer F.W., Land M.L., Hauser L., Sangwan P., de Vos W.M., Janssen P.H.,
RA Smidt H.;
RT "Genome sequence of Chthoniobacter flavus Ellin428, an aerobic
RT heterotrophic soil bacterium.";
RL J. Bacteriol. 193:2902-2903(2011).
CC -!- FUNCTION: Catalyzes the addition of meso-diaminopimelic acid to the
CC nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG)
CC in the biosynthesis of bacterial cell-wall peptidoglycan.
CC {ECO:0000256|HAMAP-Rule:MF_00208}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + meso-2,6-diaminoheptanedioate + UDP-N-acetyl-alpha-D-
CC muramoyl-L-alanyl-D-glutamate = ADP + H(+) + phosphate + UDP-N-
CC acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-
CC diaminoheptanedioate; Xref=Rhea:RHEA:23676, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:57791,
CC ChEBI:CHEBI:83900, ChEBI:CHEBI:83905, ChEBI:CHEBI:456216;
CC EC=6.3.2.13; Evidence={ECO:0000256|HAMAP-Rule:MF_00208};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00208};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000256|HAMAP-Rule:MF_00208, ECO:0000256|RuleBase:RU004135}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00208,
CC ECO:0000256|RuleBase:RU004135}.
CC -!- PTM: Carboxylation is probably crucial for Mg(2+) binding and,
CC consequently, for the gamma-phosphate positioning of ATP.
CC {ECO:0000256|HAMAP-Rule:MF_00208}.
CC -!- SIMILARITY: Belongs to the MurCDEF family. MurE subfamily.
CC {ECO:0000256|ARBA:ARBA00005898, ECO:0000256|HAMAP-Rule:MF_00208}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00208}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EDY19763.1}.
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DR EMBL; ABVL01000007; EDY19763.1; -; Genomic_DNA.
DR AlphaFoldDB; B4D201; -.
DR STRING; 497964.CfE428DRAFT_2939; -.
DR eggNOG; COG0768; Bacteria.
DR eggNOG; COG0769; Bacteria.
DR InParanoid; B4D201; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000005824; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008658; F:penicillin binding; IEA:InterPro.
DR GO; GO:0008765; F:UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 3.40.710.10; DD-peptidase/beta-lactamase superfamily; 1.
DR Gene3D; 3.90.190.20; Mur ligase, C-terminal domain; 1.
DR Gene3D; 3.40.1190.10; Mur-like, catalytic domain; 1.
DR Gene3D; 3.40.1390.10; MurE/MurF, N-terminal domain; 1.
DR Gene3D; 3.90.1310.10; Penicillin-binding protein 2a (Domain 2); 1.
DR HAMAP; MF_00208; MurE; 1.
DR InterPro; IPR012338; Beta-lactam/transpept-like.
DR InterPro; IPR036565; Mur-like_cat_sf.
DR InterPro; IPR004101; Mur_ligase_C.
DR InterPro; IPR036615; Mur_ligase_C_dom_sf.
DR InterPro; IPR013221; Mur_ligase_cen.
DR InterPro; IPR000713; Mur_ligase_N.
DR InterPro; IPR035911; MurE/MurF_N.
DR InterPro; IPR005311; PBP_dimer.
DR InterPro; IPR036138; PBP_dimer_sf.
DR InterPro; IPR001460; PCN-bd_Tpept.
DR InterPro; IPR005761; UDP-N-AcMur-Glu-dNH2Pim_ligase.
DR NCBIfam; TIGR01085; murE; 1.
DR PANTHER; PTHR23135; MUR LIGASE FAMILY MEMBER; 1.
DR PANTHER; PTHR23135:SF4; UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE MURE HOMOLOG, CHLOROPLASTIC; 1.
DR Pfam; PF01225; Mur_ligase; 1.
DR Pfam; PF02875; Mur_ligase_C; 1.
DR Pfam; PF08245; Mur_ligase_M; 1.
DR Pfam; PF03717; PBP_dimer; 1.
DR Pfam; PF00905; Transpeptidase; 1.
DR SUPFAM; SSF56601; beta-lactamase/transpeptidase-like; 1.
DR SUPFAM; SSF53623; MurD-like peptide ligases, catalytic domain; 1.
DR SUPFAM; SSF53244; MurD-like peptide ligases, peptide-binding domain; 1.
DR SUPFAM; SSF63418; MurE/MurF N-terminal domain; 1.
DR SUPFAM; SSF56519; Penicillin binding protein dimerisation domain; 1.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_00208};
KW Cell cycle {ECO:0000256|ARBA:ARBA00023306, ECO:0000256|HAMAP-
KW Rule:MF_00208};
KW Cell division {ECO:0000256|ARBA:ARBA00022618, ECO:0000256|HAMAP-
KW Rule:MF_00208};
KW Cell shape {ECO:0000256|ARBA:ARBA00022960, ECO:0000256|HAMAP-
KW Rule:MF_00208};
KW Cell wall biogenesis/degradation {ECO:0000256|ARBA:ARBA00023316,
KW ECO:0000256|HAMAP-Rule:MF_00208};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00208};
KW Ligase {ECO:0000256|HAMAP-Rule:MF_00208};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00208};
KW Membrane {ECO:0000256|ARBA:ARBA00023136};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00208};
KW Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984, ECO:0000256|HAMAP-
KW Rule:MF_00208}; Reference proteome {ECO:0000313|Proteomes:UP000005824};
KW Signal {ECO:0000256|SAM:SignalP}.
FT SIGNAL 1..24
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 25..1084
FT /note="UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-
FT diaminopimelate ligase"
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5002800351"
FT DOMAIN 52..211
FT /note="Penicillin-binding protein dimerisation"
FT /evidence="ECO:0000259|Pfam:PF03717"
FT DOMAIN 256..436
FT /note="Penicillin-binding protein transpeptidase"
FT /evidence="ECO:0000259|Pfam:PF00905"
FT DOMAIN 616..688
FT /note="Mur ligase N-terminal catalytic"
FT /evidence="ECO:0000259|Pfam:PF01225"
FT DOMAIN 700..906
FT /note="Mur ligase central"
FT /evidence="ECO:0000259|Pfam:PF08245"
FT DOMAIN 926..1011
FT /note="Mur ligase C-terminal"
FT /evidence="ECO:0000259|Pfam:PF02875"
FT REGION 436..516
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 562..587
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 1001..1004
FT /note="Meso-diaminopimelate recognition motif"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT COMPBIAS 480..494
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 495..516
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 623
FT /ligand="UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-
FT glutamate"
FT /ligand_id="ChEBI:CHEBI:83900"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT BINDING 702..708
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT BINDING 744..745
FT /ligand="UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-
FT glutamate"
FT /ligand_id="ChEBI:CHEBI:83900"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT BINDING 771
FT /ligand="UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-
FT glutamate"
FT /ligand_id="ChEBI:CHEBI:83900"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT BINDING 777
FT /ligand="UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-
FT glutamate"
FT /ligand_id="ChEBI:CHEBI:83900"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT BINDING 779
FT /ligand="UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-
FT glutamate"
FT /ligand_id="ChEBI:CHEBI:83900"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT BINDING 977
FT /ligand="meso-2,6-diaminoheptanedioate"
FT /ligand_id="ChEBI:CHEBI:57791"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT BINDING 1001..1004
FT /ligand="meso-2,6-diaminoheptanedioate"
FT /ligand_id="ChEBI:CHEBI:57791"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT BINDING 1051
FT /ligand="meso-2,6-diaminoheptanedioate"
FT /ligand_id="ChEBI:CHEBI:57791"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT BINDING 1055
FT /ligand="meso-2,6-diaminoheptanedioate"
FT /ligand_id="ChEBI:CHEBI:57791"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
FT MOD_RES 811
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00208"
SQ SEQUENCE 1084 AA; 120652 MW; 71B1B5101BA4461E CRC64;
MNHTAQKRAL FSCFALAGCF TVFSARLIDL QVTKHDEYAK IALEIHGTRQ TKPAQRGRIM
DIHGESLAQN EPVRTVVADA TLINDRAEMA TLLSTALGLP HAQLMEKLSR TAYSQALKKE
MPSPYIVLKK EVPVNVTSDL SAKLVERKMR GITFETASTR VYPNEHMLCH VLGYVNGRNE
GVDGVERTMD QFLRGHDGFR YSERDRTGKE IFVYRGQERD ARNGNNVRLT IDMGLQNIVE
MEMDAAIKQF HPKSATVILM QPKTGEILAL SNRPNYNPNI QEGVPEDHRR DRAVTDGVEP
GSTFKIVTTT AALTEKLVRA DTMINCENGY FAPFHLHDHH PYPDLSVHDI LVHSSNIGAA
KLGIQLGDQR FYDYVRRFGF GERTGVNLPG EVSGIVHPLH TWSKYSITRI PMGQEVEATP
LQIVTAMSAI ANGGHLHDAA DHSRHHRRAG PRHREVSGAG NSPGRFQGGD RCRARCARGR
RQPEGHRRPR PRGRLQGRRQ DGHGAEIRRE DAPAQPRTLH RLFRRLHAGG RSRFRLPRAG
RRSTGLARQK LWRYGRRSRF LSHRRKSRTL PRAQAHGGRT HGQCDGAQRL PRSMKLDALL
SHSAIVKVVG PTDRDITHLT YDSRRVKPGT LFFALKGEKV DGTAFIDAAI AAGAEAIVTE
NATFRTRATN IVVANARNTM ADFAAAFYQN PARALKIAGV TGTNGKTTTA FLIKHICEAA
QLRCGLLGTV RYEIGDRVLP ASRTTPESLD VHEMLWQMRS AGCKACAMEV SSHALVQARV
RDVEFDAAIF TNLTQDHLDY HKTMEAYFEA KARMFSELAA QKKKQGKAII NLDDRYGAQL
VTRFGKAIPI TTYGLGVHAD FRASNVRIDF HGTSYQLDAG GRSYLVRLPL IGQFNVYNSL
AAVAAANAMG IEVRNCVLAL ANATAVPGRL EAVPAQRQFR VFVDYAHTDD ALLNVIKTCR
ELNPARLIVV FGCGGNRDKT KRPRMGAVVD QHADHAIVTS DNPRKEEPLA IIEDIKPGMR
RGNYEVIVDR REAIFKAVAM AQPRDIILIA GKGHENYQEF ADRTMPFDDV AVARQALEGK
RSED
//
