1XXX
Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005737 | cellular_component | cytoplasm |
A | 0005829 | cellular_component | cytosol |
A | 0005886 | cellular_component | plasma membrane |
A | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
A | 0009085 | biological_process | lysine biosynthetic process |
A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
A | 0016829 | molecular_function | lyase activity |
A | 0019877 | biological_process | diaminopimelate biosynthetic process |
A | 0044281 | biological_process | small molecule metabolic process |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0005886 | cellular_component | plasma membrane |
B | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
B | 0009085 | biological_process | lysine biosynthetic process |
B | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
B | 0016829 | molecular_function | lyase activity |
B | 0019877 | biological_process | diaminopimelate biosynthetic process |
B | 0044281 | biological_process | small molecule metabolic process |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0005886 | cellular_component | plasma membrane |
C | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
C | 0009085 | biological_process | lysine biosynthetic process |
C | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
C | 0016829 | molecular_function | lyase activity |
C | 0019877 | biological_process | diaminopimelate biosynthetic process |
C | 0044281 | biological_process | small molecule metabolic process |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
D | 0005886 | cellular_component | plasma membrane |
D | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
D | 0009085 | biological_process | lysine biosynthetic process |
D | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
D | 0016829 | molecular_function | lyase activity |
D | 0019877 | biological_process | diaminopimelate biosynthetic process |
D | 0044281 | biological_process | small molecule metabolic process |
E | 0005737 | cellular_component | cytoplasm |
E | 0005829 | cellular_component | cytosol |
E | 0005886 | cellular_component | plasma membrane |
E | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
E | 0009085 | biological_process | lysine biosynthetic process |
E | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
E | 0016829 | molecular_function | lyase activity |
E | 0019877 | biological_process | diaminopimelate biosynthetic process |
E | 0044281 | biological_process | small molecule metabolic process |
F | 0005737 | cellular_component | cytoplasm |
F | 0005829 | cellular_component | cytosol |
F | 0005886 | cellular_component | plasma membrane |
F | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
F | 0009085 | biological_process | lysine biosynthetic process |
F | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
F | 0016829 | molecular_function | lyase activity |
F | 0019877 | biological_process | diaminopimelate biosynthetic process |
F | 0044281 | biological_process | small molecule metabolic process |
G | 0005737 | cellular_component | cytoplasm |
G | 0005829 | cellular_component | cytosol |
G | 0005886 | cellular_component | plasma membrane |
G | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
G | 0009085 | biological_process | lysine biosynthetic process |
G | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
G | 0016829 | molecular_function | lyase activity |
G | 0019877 | biological_process | diaminopimelate biosynthetic process |
G | 0044281 | biological_process | small molecule metabolic process |
H | 0005737 | cellular_component | cytoplasm |
H | 0005829 | cellular_component | cytosol |
H | 0005886 | cellular_component | plasma membrane |
H | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
H | 0009085 | biological_process | lysine biosynthetic process |
H | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
H | 0016829 | molecular_function | lyase activity |
H | 0019877 | biological_process | diaminopimelate biosynthetic process |
H | 0044281 | biological_process | small molecule metabolic process |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG A 2001 |
Chain | Residue |
A | ALA162 |
A | HIS164 |
A | ILE167 |
A | HOH3026 |
A | HOH3080 |
A | HOH3233 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG B 2002 |
Chain | Residue |
B | HOH3072 |
B | HOH3232 |
B | ALA162 |
B | HIS164 |
B | ILE167 |
site_id | AC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG C 2003 |
Chain | Residue |
C | ALA162 |
C | HIS164 |
C | ILE167 |
C | HOH3160 |
site_id | AC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG D 2004 |
Chain | Residue |
D | ALA162 |
D | HIS164 |
D | ILE167 |
D | HOH3090 |
site_id | AC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG E 2005 |
Chain | Residue |
E | ALA162 |
E | HIS164 |
E | ILE167 |
E | HOH3038 |
site_id | AC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MG F 2006 |
Chain | Residue |
F | ALA162 |
F | HIS164 |
F | ILE167 |
site_id | AC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG G 2007 |
Chain | Residue |
G | ALA162 |
G | HIS164 |
G | ILE167 |
G | HOH3147 |
G | HOH3226 |
site_id | AC8 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG H 2008 |
Chain | Residue |
H | ALA162 |
H | HIS164 |
H | ILE167 |
H | HOH3095 |
H | HOH3184 |
site_id | AC9 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL A 2009 |
Chain | Residue |
A | LYS174 |
A | SER179 |
A | HOH3122 |
site_id | BC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CL B 2010 |
Chain | Residue |
B | PRO155 |
B | LYS174 |
B | SER179 |
B | ILE183 |
B | HOH3168 |
B | HOH3193 |
site_id | BC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL C 2011 |
Chain | Residue |
C | LYS174 |
C | SER179 |
C | ILE183 |
C | HOH3024 |
site_id | BC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL D 2012 |
Chain | Residue |
D | LYS174 |
D | SER179 |
D | ILE183 |
D | HOH3079 |
site_id | BC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL E 2013 |
Chain | Residue |
E | PRO155 |
E | LYS174 |
E | SER179 |
E | ILE183 |
site_id | BC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CL F 2014 |
Chain | Residue |
F | LYS174 |
F | SER179 |
F | ILE183 |
F | HOH3032 |
F | HOH3048 |
site_id | BC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL G 2015 |
Chain | Residue |
G | LYS174 |
G | SER179 |
G | ILE183 |
site_id | BC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL H 2016 |
Chain | Residue |
H | LYS174 |
H | SER179 |
H | ILE183 |
site_id | BC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE DTT A 3001 |
Chain | Residue |
A | ASP195 |
A | ALA197 |
A | CYS248 |
A | MET251 |
A | SER252 |
A | HOH3144 |
site_id | BC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE DTT B 3002 |
Chain | Residue |
B | ASP195 |
B | ASP196 |
B | ALA197 |
B | CYS248 |
B | SER252 |
site_id | CC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE DTT C 3003 |
Chain | Residue |
C | ASP195 |
C | ALA197 |
C | CYS248 |
C | MET251 |
C | SER252 |
site_id | CC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE DTT D 3004 |
Chain | Residue |
D | ASP195 |
D | ASP196 |
D | ALA197 |
D | CYS248 |
D | SER252 |
site_id | CC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE DTT E 3005 |
Chain | Residue |
E | ASP195 |
E | ASP196 |
E | ALA197 |
E | CYS248 |
E | SER252 |
site_id | CC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE DTT F 3006 |
Chain | Residue |
F | ASP195 |
F | ALA197 |
F | CYS248 |
F | SER252 |
site_id | CC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE DTT G 3007 |
Chain | Residue |
G | ALA197 |
G | CYS248 |
G | MET251 |
G | SER252 |
G | ASP195 |
site_id | CC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE DTT H 3008 |
Chain | Residue |
H | ASP195 |
H | ALA197 |
H | CYS248 |
H | MET251 |
H | SER252 |
H | HOH3085 |
Functional Information from PROSITE/UniProt
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 8 |
Details | ACT_SITE: Proton donor/acceptor => ECO:0000255|HAMAP-Rule:MF_00418 |
Chain | Residue | Details |
A | TYR143 | |
B | TYR143 | |
C | TYR143 | |
D | TYR143 | |
E | TYR143 | |
F | TYR143 | |
G | TYR143 | |
H | TYR143 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | ACT_SITE: Schiff-base intermediate with substrate => ECO:0000255|HAMAP-Rule:MF_00418, ECO:0000269|PubMed:21672512 |
Chain | Residue | Details |
A | LYS171 | |
B | LYS171 | |
C | LYS171 | |
D | LYS171 | |
E | LYS171 | |
F | LYS171 | |
G | LYS171 | |
H | LYS171 |
site_id | SWS_FT_FI3 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00418 |
Chain | Residue | Details |
A | ILE211 | |
B | THR55 | |
B | ILE211 | |
C | THR55 | |
C | ILE211 | |
D | THR55 | |
D | ILE211 | |
A | THR55 | |
E | ILE211 | |
F | THR55 | |
F | ILE211 | |
G | THR55 | |
G | ILE211 | |
H | THR55 | |
H | ILE211 | |
E | THR55 |
site_id | SWS_FT_FI4 |
Number of Residues | 16 |
Details | SITE: Part of a proton relay during catalysis => ECO:0000255|HAMAP-Rule:MF_00418 |
Chain | Residue | Details |
A | THR54 | |
A | TYR117 | |
B | THR54 | |
B | TYR117 | |
C | THR54 | |
C | TYR117 | |
D | THR54 | |
D | TYR117 | |
E | TYR117 | |
F | THR54 | |
F | TYR117 | |
G | THR54 | |
G | TYR117 | |
H | THR54 | |
H | TYR117 | |
E | THR54 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
A | TYR143 | |
A | ARG148 | |
A | LYS171 |
site_id | CSA10 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
B | THR54 | |
B | LYS171 | |
B | THR55 |
site_id | CSA11 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
C | THR54 | |
C | LYS171 | |
C | THR55 |
site_id | CSA12 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
D | THR54 | |
D | LYS171 | |
D | THR55 |
site_id | CSA13 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
E | THR54 | |
E | LYS171 | |
E | THR55 |
site_id | CSA14 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
F | THR54 | |
F | LYS171 | |
F | THR55 |
site_id | CSA15 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
G | THR54 | |
G | LYS171 | |
G | THR55 |
site_id | CSA16 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
H | THR54 | |
H | LYS171 | |
H | THR55 |
site_id | CSA2 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
B | TYR143 | |
B | ARG148 | |
B | LYS171 |
site_id | CSA3 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
C | TYR143 | |
C | ARG148 | |
C | LYS171 |
site_id | CSA4 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
D | TYR143 | |
D | ARG148 | |
D | LYS171 |
site_id | CSA5 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
E | TYR143 | |
E | ARG148 | |
E | LYS171 |
site_id | CSA6 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
F | TYR143 | |
F | ARG148 | |
F | LYS171 |
site_id | CSA7 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
G | TYR143 | |
G | ARG148 | |
G | LYS171 |
site_id | CSA8 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
H | TYR143 | |
H | ARG148 | |
H | LYS171 |
site_id | CSA9 |
Number of Residues | 3 |
Details | Annotated By Reference To The Literature 1dhp |
Chain | Residue | Details |
A | THR54 | |
A | LYS171 | |
A | THR55 |