2NV1 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF THE SYNTHASE SUBUNIT PDX1 (YAAD) OF PLP SYNTHASE FROM BACILLUS SUBTILIS

Authors :   M. Strohmeier, I. Tews, I. Sinning

Date :   10 Nov 06 (Deposition) - 05 Dec 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.08

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F  (2x)

Keywords :   (Beta/Alpha)8-Barrel, Synthase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Strohmeier, T. Raschle, J. Mazurkiewicz, K. Rippe, I. Sinning, T. B. Fitzpatrick, I. Tews
Structure Of A Bacterial Pyridoxal 5'-Phosphate Synthase Complex
Proc. Natl. Acad. Sci. Usa V. 103 19284 2006
PubMed-ID: 17159152 | Reference-DOI: 10.1073/PNAS.0604950103

Molecule 1 - PYRIDOXAL BIOSYNTHESIS LYASE PDXS
	Chains	:	A, B, C, D, E, F
	EC Number	:	4.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A, PET-BSPDX1-HIS6
	Expression System Strain	:	BL21 [DE3]
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	STRAIN 168
	Synonym	:	SUPEROXIDE-INDUCIBLE PROTEIN 7, SOI7

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (2x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 35)

No.	Name	Count	Type	Full Name
1	CL	12	Ligand/Ion	CHLORIDE ION
2	EDO	11	Ligand/Ion	1,2-ETHANEDIOL
3	MG	12	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 22)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	22	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (35, 35)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:137 , ARG A:138 , HOH A:4103 , HOH A:4214 , HOH A:4328	BINDING SITE FOR RESIDUE CL A 3001
02	AC2	SOFTWARE	GLY A:214 , HOH A:4186	BINDING SITE FOR RESIDUE CL A 3002
03	AC3	SOFTWARE	HOH A:4001 , HOH A:4002 , HOH A:4003 , HOH A:4004 , HOH F:4004 , HOH F:4005	BINDING SITE FOR RESIDUE MG A 3003
04	AC4	SOFTWARE	HOH A:4005 , HOH A:4006 , HOH A:4007 , HOH A:4008 , HOH A:4009 , HOH A:4010	BINDING SITE FOR RESIDUE MG A 3004
05	AC5	SOFTWARE	ARG B:137 , ARG B:138 , HOH B:4100 , HOH B:4327	BINDING SITE FOR RESIDUE CL B 3007
06	AC6	SOFTWARE	GLY B:153 , GLY B:214 , HOH B:4177	BINDING SITE FOR RESIDUE CL B 3008
07	AC7	SOFTWARE	HOH A:4011 , HOH A:4012 , HOH A:4013 , HOH B:4014 , HOH B:4015 , HOH B:4016	BINDING SITE FOR RESIDUE MG A 3009
08	AC8	SOFTWARE	HOH B:4017 , HOH B:4018 , HOH B:4019 , HOH B:4020 , HOH B:4021 , HOH B:4022	BINDING SITE FOR RESIDUE MG B 3010
09	AC9	SOFTWARE	ARG C:137 , ARG C:138 , HOH C:4107 , HOH C:4312	BINDING SITE FOR RESIDUE CL C 3013
10	BC1	SOFTWARE	GLY C:214	BINDING SITE FOR RESIDUE CL C 3014
11	BC2	SOFTWARE	HOH B:4023 , HOH B:4024 , HOH C:4026 , HOH C:4027 , HOH C:4028 , HOH C:4029	BINDING SITE FOR RESIDUE MG C 3015
12	BC3	SOFTWARE	HOH C:4030 , HOH C:4031 , HOH C:4032 , HOH C:4033 , HOH C:4034 , HOH C:4035	BINDING SITE FOR RESIDUE MG C 3016
13	BC4	SOFTWARE	ARG D:137 , ARG D:138 , HOH D:4113 , HOH D:4411	BINDING SITE FOR RESIDUE CL D 3020
14	BC5	SOFTWARE	GLY D:153 , GLY D:214 , HOH D:4128 , HOH D:4171	BINDING SITE FOR RESIDUE CL D 3021
15	BC6	SOFTWARE	HOH C:4036 , HOH C:4037 , HOH C:4038 , HOH D:4038 , HOH D:4039 , HOH D:4040	BINDING SITE FOR RESIDUE MG C 3022
16	BC7	SOFTWARE	HOH D:4041 , HOH D:4042 , HOH D:4043 , HOH D:4044 , HOH D:4045 , HOH D:4046	BINDING SITE FOR RESIDUE MG D 3023
17	BC8	SOFTWARE	ARG E:137 , ARG E:138 , HOH E:4141	BINDING SITE FOR RESIDUE CL E 3025
18	BC9	SOFTWARE	GLY E:153 , GLY E:214 , HOH E:4190 , HOH E:4428	BINDING SITE FOR RESIDUE CL E 3026
19	CC1	SOFTWARE	HOH D:4047 , HOH D:4048 , HOH E:4049 , HOH E:4050 , HOH E:4051 , HOH E:4052	BINDING SITE FOR RESIDUE MG D 3027
20	CC2	SOFTWARE	HOH E:4053 , HOH E:4054 , HOH E:4055 , HOH E:4056 , HOH E:4057 , HOH E:4058	BINDING SITE FOR RESIDUE MG E 3028
21	CC3	SOFTWARE	ARG F:137 , ARG F:138 , HOH F:4096	BINDING SITE FOR RESIDUE CL F 3030
22	CC4	SOFTWARE	GLY F:153 , GLY F:214 , HOH F:4254	BINDING SITE FOR RESIDUE CL F 3031
23	CC5	SOFTWARE	HOH E:4059 , HOH E:4060 , HOH E:4061 , HOH F:4006 , HOH F:4007 , HOH F:4008	BINDING SITE FOR RESIDUE MG E 3032
24	CC6	SOFTWARE	HOH F:4009 , HOH F:4010 , HOH F:4011 , HOH F:4012 , HOH F:4013 , HOH F:4014	BINDING SITE FOR RESIDUE MG F 3033
25	CC7	SOFTWARE	ALA A:186 , LYS A:187 , GLY A:190 , ALA A:191 , PRO A:192 , TYR A:193 , HOH A:4334	BINDING SITE FOR RESIDUE EDO A 3005
26	CC8	SOFTWARE	LYS A:187 , ASN A:188 , GLY A:190 , HOH A:4065 , HOH A:4178 , HOH A:4211	BINDING SITE FOR RESIDUE EDO A 3006
27	CC9	SOFTWARE	LYS B:187 , HOH B:4347 , LYS F:187 , ASN F:188 , LEU F:189 , GLY F:190	BINDING SITE FOR RESIDUE EDO B 3011
28	DC1	SOFTWARE	LYS B:187 , ALA B:191 , PRO B:192 , TYR B:193 , GLY F:190 , PRO F:192 , EDO F:3035	BINDING SITE FOR RESIDUE EDO B 3012
29	DC2	SOFTWARE	PRO C:192 , TYR C:193 , GLU C:194 , LEU C:195 , HOH C:4139 , HOH C:4214 , PRO E:192 , TYR E:193 , GLU E:194	BINDING SITE FOR RESIDUE EDO C 3017
30	DC3	SOFTWARE	ALA C:186 , LYS C:187 , ALA C:191 , PRO C:192 , TYR C:193 , GLY E:190 , PRO E:192	BINDING SITE FOR RESIDUE EDO C 3018
31	DC4	SOFTWARE	ASP C:24 , LYS C:81 , ASP C:102 , ARG C:147 , PHE C:233	BINDING SITE FOR RESIDUE EDO C 3019
32	DC5	SOFTWARE	ALA D:186 , LYS D:187 , GLY D:190 , ALA D:191 , PRO D:192 , TYR D:193	BINDING SITE FOR RESIDUE EDO D 3024
33	DC6	SOFTWARE	GLY C:190 , PRO C:192 , LYS E:187 , ALA E:191 , PRO E:192 , TYR E:193	BINDING SITE FOR RESIDUE EDO E 3029
34	DC7	SOFTWARE	PRO B:192 , TYR B:193 , GLU B:194 , PRO F:192 , TYR F:193 , GLU F:194 , LEU F:195 , HOH F:4158	BINDING SITE FOR RESIDUE EDO F 3034
35	DC8	SOFTWARE	GLY B:190 , ALA B:191 , PRO B:192 , EDO B:3012 , ALA F:186 , LYS F:187 , ALA F:191 , PRO F:192 , TYR F:193	BINDING SITE FOR RESIDUE EDO F 3035

(no "SS Bond" information available for 2NV1)

(no "Cis Peptide Bond" information available for 2NV1)

(no "SAP(SNP)/Variant" information available for 2NV1)

Asymmetric Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDXS_SNZ_2	PS51129	PdxS/SNZ family profile.	PDXS_BACSU	9-294	4	A:9-271 C:9-271 D:9-272 E:9-270
2	PDXS_SNZ_1	PS01235	PdxS/SNZ family signature.	PDXS_BACSU	205-223	6	A:205-223 B:205-223 C:205-223 D:205-223 E:205-223 F:205-223

Biological Unit 1 (2, 20)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDXS_SNZ_2	PS51129	PdxS/SNZ family profile.	PDXS_BACSU	9-294	8	A:9-271 C:9-271 D:9-272 E:9-270
2	PDXS_SNZ_1	PS01235	PdxS/SNZ family signature.	PDXS_BACSU	205-223	12	A:205-223 B:205-223 C:205-223 D:205-223 E:205-223 F:205-223

(no "Exon" information available for 2NV1)

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:259
 aligned with PDXS_BACSU | P37527 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:266
                                    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      
           PDXS_BACSU     6 TERVKRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALERVPADIRAAGGVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKEL 271
               SCOP domains d2nv1a_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeee...-------........hhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....ee......hhhhhhhhhhh....eeehhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PDXS_SNZ_2  PDB: A:9-271 UniProt: 9-294                                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nv1 A   6 TERVKRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALER-------AGGVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKEL 271
                                    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      
                                                                    47      55

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with PDXS_BACSU | P37527 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:261
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 
           PDXS_BACSU    10 KRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALERVPADIRAAGGVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKE 270
               SCOP domains d2nv1b_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh....eeeee.hhhhhhhhhhhh..eeee...---------......hhhhhhhhhhhh...eeeee...hhhhhhhhhhh...eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....ee......hhhhhhhhhhh....eeehhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PDXS_SNZ_2  PDB: - UniProt: 9-294                                                                                                                                                                                                                                     PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ----------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nv1 B  10 KRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALER---------GVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKE 270
                                    19        29        39       | -       |59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 
                                                                47        57

Chain C from PDB  Type:PROTEIN  Length:256
 aligned with PDXS_BACSU | P37527 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:265
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266     
           PDXS_BACSU     7 ERVKRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALERVPADIRAAGGVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKEL 271
               SCOP domains d2nv1c_ C: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh....eeeee.hhhhhhhhhhhh..eeee...---------......hhhhhhhhhhhh...eeeee...hhhhhhhhhhh...eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....ee......hhhhhhhhhhh....eeehhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PDXS_SNZ_2  PDB: C:9-271 UniProt: 9-294                                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nv1 C   7 ERVKRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALER---------GVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKEL 271
                                    16        26        36        46|        -|       66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266     
                                                                   47        57

Chain D from PDB  Type:PROTEIN  Length:256
 aligned with PDXS_BACSU | P37527 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:265
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267     
           PDXS_BACSU     8 RVKRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALERVPADIRAAGGVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKELG 272
               SCOP domains d2nv1d_ D: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh....eeeee.hhhhhhhhhhh...eeee...---------......hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh..eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....ee......hhhhhhhhhhh....eeehhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PDXS_SNZ_2  PDB: D:9-272 UniProt: 9-294                                                                                                                                                                                                                                  PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nv1 D   8 RVKRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALER---------GVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKELG 272
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267     
                                                                  47        57

Chain E from PDB  Type:PROTEIN  Length:256
 aligned with PDXS_BACSU | P37527 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:265
                                    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     
           PDXS_BACSU     6 TERVKRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALERVPADIRAAGGVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKE 270
               SCOP domains d2nv1e_ E: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh....eeeee.hhhhhhhhhhhh..eeee...---------......hhhhhhhhhhhh...eeeee...hhhhhhhhhhh...eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....ee......hhhhhhhhhhh....eeehhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PDXS_SNZ_2  PDB: E:9-270 UniProt: 9-294                                                                                                                                                                                                                                PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ----------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nv1 E   6 TERVKRGMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALER---------GVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKE 270
                                    15        25        35        45 |       - |      65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265     
                                                                    47        57

Chain F from PDB  Type:PROTEIN  Length:250
 aligned with PDXS_BACSU | P37527 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:260
                                    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
           PDXS_BACSU    12 GMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALERVPADIRAAGGVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKEL 271
               SCOP domains d2nv1f_ F: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SOR_SNZ-2nv1F01 F:12-212                                                                                                                                                                                 ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) SOR_SNZ-2nv1F02 F:12-212                                                                                                                                                                                 ----------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) SOR_SNZ-2nv1F03 F:12-212                                                                                                                                                                                 ----------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) SOR_SNZ-2nv1F04 F:12-212                                                                                                                                                                                 ----------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) SOR_SNZ-2nv1F05 F:12-212                                                                                                                                                                                 ----------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) SOR_SNZ-2nv1F06 F:12-212                                                                                                                                                                                 ----------------------------------------------------------- Pfam domains (6)
         Sec.struct. author ..hhhhh..eeeee.hhhhhhhhhhhh..eeee..----------......hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh..eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....eeee....hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PDXS_SNZ_2  PDB: - UniProt: 9-294                                                                                                                                                                                                                                    PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDXS_SNZ_1         ------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nv1 F  12 GMAEMQKGGVIMDVINAEQAKIAEEAGAVAVMALE----------GVARMADPTIVEEVMNAVSIPVMAKARIGHIVEARVLEAMGVDYIDESEVLTPADEEFHLNKNEYTVPFVCGCRDLGEATRRIAEGASMLRTKGEPGTGNIVEAVRHMRKVNAQVRKVVAMSEDELMTEAKNLGAPYELLLQIKKDGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSDNPAKFAKAIVEATTHFTDYKLIAELSKEL 271
                                    21        31        41    |    -     |  61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
                                                             46         57

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: PdxS-like (6)

Protein domain: automated matches (5)

Bacillus subtilis [TaxId: 1423] (2)

1a	d2nv1a_	A:
1b	d2nv1b_	B:
1c	d2nv1c_	C:
1d	d2nv1d_	D:
1e	d2nv1e_	E:
1f	d2nv1f_	F:

(no "CATH Domain" information available for 2NV1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: SOR_SNZ (6)

Bacillus subtilis (2)

1a	SOR_SNZ-2nv1F01	F:12-212
1b	SOR_SNZ-2nv1F02	F:12-212
1c	SOR_SNZ-2nv1F03	F:12-212
1d	SOR_SNZ-2nv1F04	F:12-212
1e	SOR_SNZ-2nv1F05	F:12-212
1f	SOR_SNZ-2nv1F06	F:12-212

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (PDXS_BACSU | P37527)

molecular function
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0036381	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity	Catalysis of the reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate. The reaction occurs in two steps: L-glutamine + H2O = L-glutamate + NH3, and subsequently D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5'-phosphate + 4 H2O + phosphate.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0042823	pyridoxal phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
	GO:0042819	vitamin B6 biosynthetic process	The chemical reactions and pathways resulting in the formation of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2nv1)

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	2nv1
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	PDXS_BACSU \| P37527	:	2nv2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 35)

Sites (35, 35)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 10)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 6)

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Pfam Domains (1, 6)

Gene Ontology (6, 6)

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