Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE MENAQUINONE BIOSYNTHESIS PROTEIN MEND FROM BACILLUS SUBTILIS
 
Authors :  A. Dawson, M. Chen, P. K. Fyfe, Z. Guo, W. N. Hunter
Date :  01 Mar 10  (Deposition) - 14 Jul 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transferase, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dawson, M. Chen, P. K. Fyfe, Z. Guo, W. N. Hunter
Structure And Reactivity Of Bacillus Subtilis Mend Catalyzing The First Committed Step In Menaquinone Biosynthesis.
J. Mol. Biol. V. 401 253 2010
PubMed-ID: 20600129  |  Reference-DOI: 10.1016/J.JMB.2010.06.025

(-) Compounds

Molecule 1 - 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
    Atcc: 23857
    Chains: A, B, C, D
    EC Number: 2.2.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15BTEV_BSMEND
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: MENAQUINONE BIOSYNTHESIS PROTEIN MEND, SEPHCHC SYNTHASE, MEND

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 24)

Asymmetric/Biological Unit (5, 24)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MN4Ligand/IonMANGANESE (II) ION
3NA4Ligand/IonSODIUM ION
4SO48Ligand/IonSULFATE ION
5TPP4Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:405 , MET A:406 , ASN A:431 , ILE A:433 , ASP A:434 , GLY A:456 , ASP A:457 , LEU A:458 , SER A:459 , ASN A:484 , GLY A:486 , GLY A:487 , GLY A:488 , ILE A:489 , PHE A:490 , MN A:602 , HOH A:2200 , HOH A:2213 , HOH A:2237 , HOH A:2282 , GLU B:54 , GLN B:117 , EDO B:603BINDING SITE FOR RESIDUE TPP A 601
02AC2SOFTWAREASP A:457 , ASN A:484 , GLY A:486 , TPP A:601 , HOH A:2237BINDING SITE FOR RESIDUE MN A 602
03AC3SOFTWAREGLY A:30 , SER A:31 , ARG A:32 , THR A:77 , ARG A:106 , GLN A:117 , PHE B:490 , TPP B:601BINDING SITE FOR RESIDUE EDO A 603
04AC4SOFTWAREGLU A:54 , GLN A:117 , EDO A:603 , SER B:405 , MET B:406 , ASN B:431 , ILE B:433 , ASP B:434 , GLY B:456 , ASP B:457 , LEU B:458 , SER B:459 , ASN B:484 , GLY B:486 , GLY B:487 , GLY B:488 , ILE B:489 , MN B:602 , HOH B:2155 , HOH B:2238 , HOH B:2239BINDING SITE FOR RESIDUE TPP B 601
05AC5SOFTWAREASP B:457 , ASN B:484 , GLY B:486 , TPP B:601 , HOH B:2239BINDING SITE FOR RESIDUE MN B 602
06AC6SOFTWAREPHE A:490 , TPP A:601 , GLY B:30 , SER B:31 , ARG B:32 , THR B:77 , GLN B:117BINDING SITE FOR RESIDUE EDO B 603
07AC7SOFTWARESER C:405 , MET C:406 , PRO C:407 , ASN C:431 , GLY C:432 , ILE C:433 , ASP C:434 , GLY C:456 , ASP C:457 , LEU C:458 , SER C:459 , ASN C:484 , GLY C:486 , GLY C:487 , GLY C:488 , ILE C:489 , PHE C:490 , MN C:602 , HOH C:2251 , HOH C:2252 , HOH C:2253 , PRO D:29 , GLU D:54 , THR D:80 , GLN D:117 , EDO D:603BINDING SITE FOR RESIDUE TPP C 601
08AC8SOFTWAREASP C:457 , ASN C:484 , GLY C:486 , TPP C:601 , HOH C:2253BINDING SITE FOR RESIDUE MN C 602
09AC9SOFTWAREGLY C:30 , SER C:31 , ARG C:32 , THR C:77 , GLN C:117 , PHE D:490 , TPP D:601BINDING SITE FOR RESIDUE EDO C 603
10BC1SOFTWAREPRO C:29 , GLU C:54 , THR C:80 , GLN C:117 , EDO C:603 , SER D:405 , MET D:406 , ASN D:431 , ILE D:433 , ASP D:434 , GLY D:456 , ASP D:457 , LEU D:458 , SER D:459 , ASN D:484 , GLY D:486 , GLY D:487 , GLY D:488 , ILE D:489 , PHE D:490 , MN D:602 , HOH D:2206 , HOH D:2290 , HOH D:2291 , HOH D:2292BINDING SITE FOR RESIDUE TPP D 601
11BC2SOFTWAREASP D:457 , ASN D:484 , GLY D:486 , TPP D:601 , HOH D:2292BINDING SITE FOR RESIDUE MN D 602
12BC3SOFTWAREPHE C:490 , TPP C:601 , GLY D:30 , SER D:31 , ARG D:32 , THR D:77 , GLN D:117BINDING SITE FOR RESIDUE EDO D 603
13BC4SOFTWARECYS D:40 , ALA D:41 , HIS D:43 , ILE D:46BINDING SITE FOR RESIDUE NA D1581
14BC5SOFTWARECYS A:40 , ALA A:41 , HIS A:43 , ILE A:46BINDING SITE FOR RESIDUE NA A1581
15BC6SOFTWARECYS B:40 , ALA B:41 , HIS B:43 , ILE B:46 , HOH B:2022 , HOH B:2024BINDING SITE FOR RESIDUE NA B1581
16BC7SOFTWARECYS C:40 , ALA C:41 , HIS C:43 , ILE C:46 , HOH C:2015BINDING SITE FOR RESIDUE NA C1579
17BC8SOFTWAREARG A:32 , PRO A:107 , LEU A:110 , LEU A:173 , ARG A:174 , GLU A:175 , HOH A:2283BINDING SITE FOR RESIDUE SO4 A1582
18BC9SOFTWAREARG B:32 , PRO B:107 , LEU B:110 , LEU B:173 , ARG B:174 , GLU B:175BINDING SITE FOR RESIDUE SO4 B1582
19CC1SOFTWAREARG D:32 , PRO D:107 , LEU D:110 , ARG D:174 , GLU D:175 , HOH D:2041 , HOH D:2293BINDING SITE FOR RESIDUE SO4 D1582
20CC2SOFTWAREARG C:32 , PRO C:107 , GLU C:109 , LEU C:110 , LEU C:173 , ARG C:174 , GLU C:175 , HOH C:2254 , HOH C:2255BINDING SITE FOR RESIDUE SO4 C1580
21CC3SOFTWARELYS A:276 , ARG A:564 , HOH A:2284 , HOH A:2285BINDING SITE FOR RESIDUE SO4 A1583
22CC4SOFTWARELYS B:276 , ARG B:564 , HOH B:2121BINDING SITE FOR RESIDUE SO4 B1583
23CC5SOFTWARELYS C:276 , PHE C:492 , ARG C:564 , HOH C:2256BINDING SITE FOR RESIDUE SO4 C1581
24CC6SOFTWARELYS D:276 , PHE D:492 , ARG D:564BINDING SITE FOR RESIDUE SO4 D1583

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X7J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X7J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X7J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X7J)

(-) Exons   (0, 0)

(no "Exon" information available for 2X7J)

(-) 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:579
 aligned with MEND_BACSU | P23970 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:579
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571         
           MEND_BACSU     2 TVNPITHYIGSFIDEFALSGITDAVVCPGSRSTPLAVLCAAHPDISVHVQIDERSAGFFALGLAKAKQRPVLLICTSGTAAANFYPAVVEAHYSRVPIIVLTADRPHELREVGAPQAINQHFLFGNFVKFFTDSALPEESPQMLRYIRTLASRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGTQSVDRESLSDVAEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILADPLSNLRNGVHDKSTVIDAYDSFLKDDELKRKLRPDVVIRFGPMPVSKPVFLWLKDDPTIQQIVIDEDGGWRDPTQASAHMIHCNASVFAEEIMAGLTAATRSSEWLEKWQFVNGRFREHLQTISSEDVSFEGNLYRILQHLVPENSSLFVGNSMPIRDVDTFFEKQDRPFRIYSNRGANGIDGVVSSAMGVCEGTKAPVTLVIGDLSFYHDLNGLLAAKKLGIPLTVILVNNDGGGIFSFLPQASEKTHFEDLFGTPTGLDFKHAAALYGGTYSCPASWDEFKTAYAPQADKPGLHLIEIKTDRQSRVQLHRDMLNEAVREVKKQWEL 580
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.............hhhhh..eee......hhhhhhhhhhhhhhhhhhhhh....eeeeeee.......................eee..eee..hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..eee.hhhh..........ee.hhhhhh.hhhhhhhhh..eeeee.....hhhhhhhhhhh...eeeee..............eee..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh....eeee..hhhhhhhhhhh.......eee.........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhh..eee...hhhhhhhhh........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x7j A   2 TVNPITHYIGSFIDEFALSGITDAVVCPGSRSTPLAVLCAAHPDISVHVQIDERSAGFFALGLAKAKQRPVLLICTSGTAAANFYPAVVEAHYSRVPIIVLTADRPHELREVGAPQAINQHFLFGNFVKFFTDSALPEESPQMLRYIRTLASRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGTQSVDRESLSDVAEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILADPLSNLRNGVHDKSTVIDAYDSFLKDDELKRKLRPDVVIRFGPMPVSKPVFLWLKDDPTIQQIVIDEDGGWRDPTQASAHMIHCNASVFAEEIMAGLTAATRSSEWLEKWQFVNGRFREHLQTISSEDVSFEGNLYRILQHLVPENSSLFVGNSMPIRDVDTFFEKQDRPFRIYSNRGANGIDGVVSSAMGVCEGTKAPVTLVIGDLSFYHDLNGLLAAKKLGIPLTVILVNNDGGGIFSFLPQASEKTHFEDLFGTPTGLDFKHAAALYGGTYSCPASWDEFKTAYAPQADKPGLHLIEIKTDRQSRVQLHRDMLNEAVREVKKQWEL 580
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571         


Chain B from PDB  Type:PROTEIN  Length:579
 aligned with MEND_BACSU | P23970 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:579
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571         
           MEND_BACSU     2 TVNPITHYIGSFIDEFALSGITDAVVCPGSRSTPLAVLCAAHPDISVHVQIDERSAGFFALGLAKAKQRPVLLICTSGTAAANFYPAVVEAHYSRVPIIVLTADRPHELREVGAPQAINQHFLFGNFVKFFTDSALPEESPQMLRYIRTLASRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGTQSVDRESLSDVAEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILADPLSNLRNGVHDKSTVIDAYDSFLKDDELKRKLRPDVVIRFGPMPVSKPVFLWLKDDPTIQQIVIDEDGGWRDPTQASAHMIHCNASVFAEEIMAGLTAATRSSEWLEKWQFVNGRFREHLQTISSEDVSFEGNLYRILQHLVPENSSLFVGNSMPIRDVDTFFEKQDRPFRIYSNRGANGIDGVVSSAMGVCEGTKAPVTLVIGDLSFYHDLNGLLAAKKLGIPLTVILVNNDGGGIFSFLPQASEKTHFEDLFGTPTGLDFKHAAALYGGTYSCPASWDEFKTAYAPQADKPGLHLIEIKTDRQSRVQLHRDMLNEAVREVKKQWEL 580
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh....................eee......hhhhhhhhhhhhhhhhhhhhh....eeeeeee.......................eee..eee.hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..eee.hhhh..........ee.hhhhhh.hhhhhhhh...eeeee.....hhhhhhhhhhh...eeeee..............eee..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......eeee..hhhhhhhhhhh.......eee.........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhh..hhhhhh.......hhhhhhhh..eee...hhhhhhhhh........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x7j B   2 TVNPITHYIGSFIDEFALSGITDAVVCPGSRSTPLAVLCAAHPDISVHVQIDERSAGFFALGLAKAKQRPVLLICTSGTAAANFYPAVVEAHYSRVPIIVLTADRPHELREVGAPQAINQHFLFGNFVKFFTDSALPEESPQMLRYIRTLASRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGTQSVDRESLSDVAEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILADPLSNLRNGVHDKSTVIDAYDSFLKDDELKRKLRPDVVIRFGPMPVSKPVFLWLKDDPTIQQIVIDEDGGWRDPTQASAHMIHCNASVFAEEIMAGLTAATRSSEWLEKWQFVNGRFREHLQTISSEDVSFEGNLYRILQHLVPENSSLFVGNSMPIRDVDTFFEKQDRPFRIYSNRGANGIDGVVSSAMGVCEGTKAPVTLVIGDLSFYHDLNGLLAAKKLGIPLTVILVNNDGGGIFSFLPQASEKTHFEDLFGTPTGLDFKHAAALYGGTYSCPASWDEFKTAYAPQADKPGLHLIEIKTDRQSRVQLHRDMLNEAVREVKKQWEL 580
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571         


Chain C from PDB  Type:PROTEIN  Length:577
 aligned with MEND_BACSU | P23970 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:577
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       
           MEND_BACSU     2 TVNPITHYIGSFIDEFALSGITDAVVCPGSRSTPLAVLCAAHPDISVHVQIDERSAGFFALGLAKAKQRPVLLICTSGTAAANFYPAVVEAHYSRVPIIVLTADRPHELREVGAPQAINQHFLFGNFVKFFTDSALPEESPQMLRYIRTLASRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGTQSVDRESLSDVAEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILADPLSNLRNGVHDKSTVIDAYDSFLKDDELKRKLRPDVVIRFGPMPVSKPVFLWLKDDPTIQQIVIDEDGGWRDPTQASAHMIHCNASVFAEEIMAGLTAATRSSEWLEKWQFVNGRFREHLQTISSEDVSFEGNLYRILQHLVPENSSLFVGNSMPIRDVDTFFEKQDRPFRIYSNRGANGIDGVVSSAMGVCEGTKAPVTLVIGDLSFYHDLNGLLAAKKLGIPLTVILVNNDGGGIFSFLPQASEKTHFEDLFGTPTGLDFKHAAALYGGTYSCPASWDEFKTAYAPQADKPGLHLIEIKTDRQSRVQLHRDMLNEAVREVKKQW 578
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.............hhhhh..eee......hhhhhhhhhhhhhhhhhhhhh....eeeeeee.......................eee..eee..hhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eee.hhhh..........ee.hhhhhh.hhhhhhhh...eeeee.....hhhhhhhhhhh...eeeee..............eee..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh....eeee..hhhhhhhhhhh.......eeee........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhh..eee...hhhhhhhhh........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x7j C   2 TVNPITHYIGSFIDEFALSGITDAVVCPGSRSTPLAVLCAAHPDISVHVQIDERSAGFFALGLAKAKQRPVLLICTSGTAAANFYPAVVEAHYSRVPIIVLTADRPHELREVGAPQAINQHFLFGNFVKFFTDSALPEESPQMLRYIRTLASRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGTQSVDRESLSDVAEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILADPLSNLRNGVHDKSTVIDAYDSFLKDDELKRKLRPDVVIRFGPMPVSKPVFLWLKDDPTIQQIVIDEDGGWRDPTQASAHMIHCNASVFAEEIMAGLTAATRSSEWLEKWQFVNGRFREHLQTISSEDVSFEGNLYRILQHLVPENSSLFVGNSMPIRDVDTFFEKQDRPFRIYSNRGANGIDGVVSSAMGVCEGTKAPVTLVIGDLSFYHDLNGLLAAKKLGIPLTVILVNNDGGGIFSFLPQASEKTHFEDLFGTPTGLDFKHAAALYGGTYSCPASWDEFKTAYAPQADKPGLHLIEIKTDRQSRVQLHRDMLNEAVREVKKQW 578
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       


Chain D from PDB  Type:PROTEIN  Length:579
 aligned with MEND_BACSU | P23970 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:579
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571         
           MEND_BACSU     2 TVNPITHYIGSFIDEFALSGITDAVVCPGSRSTPLAVLCAAHPDISVHVQIDERSAGFFALGLAKAKQRPVLLICTSGTAAANFYPAVVEAHYSRVPIIVLTADRPHELREVGAPQAINQHFLFGNFVKFFTDSALPEESPQMLRYIRTLASRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGTQSVDRESLSDVAEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILADPLSNLRNGVHDKSTVIDAYDSFLKDDELKRKLRPDVVIRFGPMPVSKPVFLWLKDDPTIQQIVIDEDGGWRDPTQASAHMIHCNASVFAEEIMAGLTAATRSSEWLEKWQFVNGRFREHLQTISSEDVSFEGNLYRILQHLVPENSSLFVGNSMPIRDVDTFFEKQDRPFRIYSNRGANGIDGVVSSAMGVCEGTKAPVTLVIGDLSFYHDLNGLLAAKKLGIPLTVILVNNDGGGIFSFLPQASEKTHFEDLFGTPTGLDFKHAAALYGGTYSCPASWDEFKTAYAPQADKPGLHLIEIKTDRQSRVQLHRDMLNEAVREVKKQWEL 580
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------TPP_enzyme_N-2x7jD05 D:12-180                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_enzyme_C-2x7jD01 D:409-552                                                                                                                  ---------------------------- Pfam domains (1)
           Pfam domains (2) ----------TPP_enzyme_N-2x7jD06 D:12-180                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_enzyme_C-2x7jD02 D:409-552                                                                                                                  ---------------------------- Pfam domains (2)
           Pfam domains (3) ----------TPP_enzyme_N-2x7jD07 D:12-180                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_enzyme_C-2x7jD03 D:409-552                                                                                                                  ---------------------------- Pfam domains (3)
           Pfam domains (4) ----------TPP_enzyme_N-2x7jD08 D:12-180                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_enzyme_C-2x7jD04 D:409-552                                                                                                                  ---------------------------- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.............hhhhh..eee......hhhhhhhhhhhhhhhhhhhhh....eeeeeee.......................eee..eee.....hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..eee.hhhh..........ee.hhhhhh.hhhhhhhhh..eeeee.....hhhhhhhhhhh...eeeee..............eee..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......eeee..hhhhhhhhhhh.......eee.........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhh..eee...hhhhhhhhh........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x7j D   2 TVNPITHYIGSFIDEFALSGITDAVVCPGSRSTPLAVLCAAHPDISVHVQIDERSAGFFALGLAKAKQRPVLLICTSGTAAANFYPAVVEAHYSRVPIIVLTADRPHELREVGAPQAINQHFLFGNFVKFFTDSALPEESPQMLRYIRTLASRAAGEAQKRPMGPVHVNVPLREPLMPDLSDEPFGRMRTGRHVSVKTGTQSVDRESLSDVAEMLAEAEKGMIVCGELHSDADKENIIALSKALQYPILADPLSNLRNGVHDKSTVIDAYDSFLKDDELKRKLRPDVVIRFGPMPVSKPVFLWLKDDPTIQQIVIDEDGGWRDPTQASAHMIHCNASVFAEEIMAGLTAATRSSEWLEKWQFVNGRFREHLQTISSEDVSFEGNLYRILQHLVPENSSLFVGNSMPIRDVDTFFEKQDRPFRIYSNRGANGIDGVVSSAMGVCEGTKAPVTLVIGDLSFYHDLNGLLAAKKLGIPLTVILVNNDGGGIFSFLPQASEKTHFEDLFGTPTGLDFKHAAALYGGTYSCPASWDEFKTAYAPQADKPGLHLIEIKTDRQSRVQLHRDMLNEAVREVKKQWEL 580
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571
   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 2X7J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X7J)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: THDP-binding (106)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (MEND_BACSU | P23970)
molecular function
    GO:0070204    2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity    Catalysis of the reaction: 2-oxoglutarate + H(+) + isochorismate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO(2).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TPP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2x7j)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2x7j
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MEND_BACSU | P23970
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.2.1.9
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MEND_BACSU | P23970
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2X7J)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2X7J)