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3FA3
Asym. Unit
Info
Asym.Unit (728 KB)
Biol.Unit 1 (187 KB)
Biol.Unit 2 (190 KB)
Biol.Unit 3 (184 KB)
Biol.Unit 4 (185 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 2,3-DIMETHYLMALATE LYASE, A PEP MUTASE/ISOCITRATE LYASE SUPERFAMILY MEMBER, TRIGONAL CRYSTAL FORM
Authors
:
B. C. Narayanan, O. Herzberg
Date
:
14 Nov 08 (Deposition) - 27 Jan 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Keywords
:
Alpha/Beta Barrel, Helix Swapping, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Narayanan, W. Niu, H. J. Joosten, Z. Li, R. K. Kuipers, P. J. Schaap, D. Dunaway-Mariano, O. Herzberg
Structure And Function Of 2, 3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member.
J. Mol. Biol. V. 386 486 2009
[
close entry info
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Hetero Components
(3, 35)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
2i: MANGANESE (II) ION (MNi)
2j: MANGANESE (II) ION (MNj)
2k: MANGANESE (II) ION (MNk)
2l: MANGANESE (II) ION (MNl)
2m: MANGANESE (II) ION (MNm)
2n: MANGANESE (II) ION (MNn)
2o: MANGANESE (II) ION (MNo)
2p: MANGANESE (II) ION (MNp)
3a: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFa)
3b: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFb)
3c: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFc)
3d: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFd)
3e: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFe)
3f: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFf)
3g: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFg)
3h: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFh)
3i: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFi)
3j: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFj)
3k: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFk)
3l: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFl)
3m: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFm)
3n: 2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDI... (OAFn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
5
Ligand/Ion
GLYCEROL
2
MN
16
Ligand/Ion
MANGANESE (II) ION
3
OAF
14
Ligand/Ion
2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDIOIC ACID
[
close Hetero Component info
]
Sites
(35, 35)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:87 , LYS A:122 , HOH A:304 , HOH A:305 , HOH A:306 , OAF A:501
BINDING SITE FOR RESIDUE MN A 401
02
AC2
SOFTWARE
TYR A:44 , THR A:46 , GLY A:47 , ALA A:48 , ASP A:59 , ASP A:87 , CYS A:124 , GLY A:125 , HIS A:126 , ARG A:161 , GLU A:191 , ASN A:214 , VAL A:216 , PRO A:240 , HOH A:305 , HOH A:306 , MN A:401
BINDING SITE FOR RESIDUE OAF A 501
03
AC3
SOFTWARE
MET A:74 , ASN A:77 , ILE A:78 , HOH B:617 , GLU C:103 , GLN C:104 , ARG C:107 , HOH C:319
BINDING SITE FOR RESIDUE GOL A 602
04
AC4
SOFTWARE
GLY A:39 , ASP A:41 , HOH A:814 , GLN I:290 , GLY I:298 , GLY I:299
BINDING SITE FOR RESIDUE GOL A 605
05
AC5
SOFTWARE
ASP B:87 , LYS B:122 , HOH B:306 , HOH B:307 , HOH B:308 , OAF B:501
BINDING SITE FOR RESIDUE MN B 401
06
AC6
SOFTWARE
TYR B:44 , THR B:46 , GLY B:47 , ALA B:48 , ASP B:59 , ASP B:87 , CYS B:124 , GLY B:125 , ARG B:161 , GLU B:191 , ASN B:214 , VAL B:216 , PRO B:240 , HOH B:306 , HOH B:307 , MN B:401
BINDING SITE FOR RESIDUE OAF B 501
07
AC7
SOFTWARE
ASP C:87 , LYS C:122 , HOH C:309 , HOH C:310 , HOH C:311 , OAF C:501
BINDING SITE FOR RESIDUE MN C 401
08
AC8
SOFTWARE
TYR C:44 , THR C:46 , GLY C:47 , ALA C:48 , ASP C:59 , ASP C:87 , CYS C:124 , GLY C:125 , HIS C:126 , ARG C:161 , GLU C:191 , ASN C:214 , PRO C:240 , HOH C:309 , MN C:401
BINDING SITE FOR RESIDUE OAF C 501
09
AC9
SOFTWARE
ASP D:87 , LYS D:122 , HOH D:312 , HOH D:313 , HOH D:314 , OAF D:501
BINDING SITE FOR RESIDUE MN D 401
10
BC1
SOFTWARE
TYR D:44 , THR D:46 , GLY D:47 , ALA D:48 , ASP D:59 , ASP D:87 , CYS D:124 , GLY D:125 , ARG D:161 , GLU D:191 , ASN D:214 , VAL D:216 , PRO D:240 , HOH D:313 , HOH D:314 , MN D:401
BINDING SITE FOR RESIDUE OAF D 501
11
BC2
SOFTWARE
ASP E:87 , LYS E:122 , HOH E:315 , HOH E:316 , HOH E:317 , OAF E:501
BINDING SITE FOR RESIDUE MN E 401
12
BC3
SOFTWARE
TYR E:44 , THR E:46 , GLY E:47 , ALA E:48 , ASP E:59 , ASP E:87 , CYS E:124 , GLY E:125 , HIS E:126 , ARG E:161 , GLU E:191 , ASN E:214 , VAL E:216 , PRO E:240 , HOH E:317 , MN E:401
BINDING SITE FOR RESIDUE OAF E 501
13
BC4
SOFTWARE
ARG E:69 , ALA E:70 , GLU E:73 , ARG G:69
BINDING SITE FOR RESIDUE GOL E 604
14
BC5
SOFTWARE
ASP F:87 , HOH F:318 , HOH F:319 , HOH F:320 , OAF F:501
BINDING SITE FOR RESIDUE MN F 401
15
BC6
SOFTWARE
TYR F:44 , THR F:46 , GLY F:47 , ALA F:48 , ASP F:59 , ASP F:87 , CYS F:124 , GLY F:125 , ARG F:161 , GLU F:191 , ASN F:214 , VAL F:216 , PRO F:240 , HOH F:318 , HOH F:319 , MN F:401
BINDING SITE FOR RESIDUE OAF F 501
16
BC7
SOFTWARE
ASP G:87 , LYS G:122 , HOH G:321 , HOH G:322 , HOH G:323 , OAF G:501
BINDING SITE FOR RESIDUE MN G 401
17
BC8
SOFTWARE
TYR G:44 , THR G:46 , GLY G:47 , ALA G:48 , ASP G:59 , ASP G:87 , CYS G:124 , GLY G:125 , HIS G:126 , ARG G:161 , GLU G:191 , ASN G:214 , VAL G:216 , PRO G:240 , HOH G:322 , HOH G:323 , MN G:401
BINDING SITE FOR RESIDUE OAF G 501
18
BC9
SOFTWARE
TYR G:27 , ASP G:28 , SER G:53 , VAL G:54 , ASN G:71 , SER H:53 , VAL H:54
BINDING SITE FOR RESIDUE GOL G 601
19
CC1
SOFTWARE
ASP H:87 , LYS H:122 , HOH H:324 , HOH H:325 , HOH H:326 , OAF H:501
BINDING SITE FOR RESIDUE MN H 401
20
CC2
SOFTWARE
TYR H:44 , THR H:46 , GLY H:47 , ALA H:48 , ASP H:59 , ASP H:87 , CYS H:124 , GLY H:125 , ARG H:161 , GLU H:191 , ASN H:214 , VAL H:216 , PRO H:240 , HOH H:325 , HOH H:326 , MN H:401
BINDING SITE FOR RESIDUE OAF H 501
21
CC3
SOFTWARE
ASP I:87 , LYS I:122 , HOH I:327 , HOH I:328 , HOH I:329 , OAF I:501
BINDING SITE FOR RESIDUE MN I 401
22
CC4
SOFTWARE
TYR I:44 , THR I:46 , GLY I:47 , ALA I:48 , ASP I:59 , ASP I:87 , CYS I:124 , GLY I:125 , HIS I:126 , ARG I:161 , GLU I:191 , ASN I:214 , VAL I:216 , PRO I:240 , HOH I:327 , HOH I:328 , HOH I:329 , MN I:401
BINDING SITE FOR RESIDUE OAF I 501
23
CC5
SOFTWARE
ASP J:87 , ASP J:89 , HOH J:330 , HOH J:331 , HOH J:809
BINDING SITE FOR RESIDUE MN J 401
24
CC6
SOFTWARE
ASP K:87 , HOH K:332 , HOH K:333 , HOH K:334 , OAF K:501
BINDING SITE FOR RESIDUE MN K 401
25
CC7
SOFTWARE
TYR K:44 , THR K:46 , GLY K:47 , ALA K:48 , ASP K:59 , ASP K:87 , CYS K:124 , GLY K:125 , ARG K:161 , GLU K:191 , ASN K:214 , VAL K:216 , PRO K:240 , HOH K:333 , MN K:401
BINDING SITE FOR RESIDUE OAF K 501
26
CC8
SOFTWARE
ASP L:87 , LYS L:122 , HOH L:336 , HOH L:337 , HOH L:338 , OAF L:501
BINDING SITE FOR RESIDUE MN L 401
27
CC9
SOFTWARE
TYR L:44 , THR L:46 , GLY L:47 , ALA L:48 , ASP L:59 , ASP L:87 , CYS L:124 , GLY L:125 , HIS L:126 , ARG L:161 , GLU L:191 , ASN L:214 , PRO L:240 , HOH L:337 , HOH L:338 , MN L:401
BINDING SITE FOR RESIDUE OAF L 501
28
DC1
SOFTWARE
ASP M:87 , LYS M:122 , HOH M:339 , HOH M:340 , HOH M:341 , OAF M:501
BINDING SITE FOR RESIDUE MN M 401
29
DC2
SOFTWARE
TYR M:44 , THR M:46 , GLY M:47 , ALA M:48 , ASP M:59 , ASP M:87 , CYS M:124 , GLY M:125 , ARG M:161 , GLU M:191 , ASN M:214 , PRO M:240 , HOH M:340 , HOH M:341 , MN M:401
BINDING SITE FOR RESIDUE OAF M 501
30
DC3
SOFTWARE
GLY E:39 , ASP E:41 , GLN M:290 , ALA M:295 , HOH M:815
BINDING SITE FOR RESIDUE GOL M 606
31
DC4
SOFTWARE
ASP N:87 , ASP N:89 , HOH N:342 , HOH N:343 , HOH N:344
BINDING SITE FOR RESIDUE MN N 401
32
DC5
SOFTWARE
ASP O:87 , HOH O:345 , HOH O:347 , HOH O:348 , OAF O:501
BINDING SITE FOR RESIDUE MN O 401
33
DC6
SOFTWARE
TYR O:44 , THR O:46 , GLY O:47 , ALA O:48 , ASP O:59 , ASP O:87 , CYS O:124 , GLY O:125 , ARG O:161 , GLU O:191 , ASN O:214 , VAL O:216 , PRO O:240 , HOH O:348 , MN O:401
BINDING SITE FOR RESIDUE OAF O 501
34
DC7
SOFTWARE
ASP P:87 , LYS P:122 , HOH P:349 , HOH P:350 , HOH P:351 , OAF P:501
BINDING SITE FOR RESIDUE MN P 401
35
DC8
SOFTWARE
TYR P:44 , THR P:46 , GLY P:47 , ALA P:48 , ASP P:59 , ASP P:87 , CYS P:124 , GLY P:125 , HIS P:126 , ARG P:161 , GLU P:191 , ASN P:214 , PRO P:240 , HOH P:351 , MN P:401
BINDING SITE FOR RESIDUE OAF P 501
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 16)
Info
All SCOP Domains
1a: SCOP_d3fa3a_ (A:)
1b: SCOP_d3fa3b_ (B:)
1c: SCOP_d3fa3c_ (C:)
1d: SCOP_d3fa3d_ (D:)
1e: SCOP_d3fa3e_ (E:)
1f: SCOP_d3fa3f_ (F:)
1g: SCOP_d3fa3g_ (G:)
1h: SCOP_d3fa3h_ (H:)
1i: SCOP_d3fa3i_ (I:)
1j: SCOP_d3fa3j_ (J:)
1k: SCOP_d3fa3k_ (K:)
1l: SCOP_d3fa3l_ (L:)
1m: SCOP_d3fa3m_ (M:)
1n: SCOP_d3fa3n_ (N:)
1o: SCOP_d3fa3o_ (O:)
1p: SCOP_d3fa3p_ (P:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Phosphoenolpyruvate/pyruvate domain
(92)
Family
:
automated matches
(16)
Protein domain
:
automated matches
(16)
Aspergillus niger [TaxId: 5061]
(2)
1a
d3fa3a_
A:
1b
d3fa3b_
B:
1c
d3fa3c_
C:
1d
d3fa3d_
D:
1e
d3fa3e_
E:
1f
d3fa3f_
F:
1g
d3fa3g_
G:
1h
d3fa3h_
H:
1i
d3fa3i_
I:
1j
d3fa3j_
J:
1k
d3fa3k_
K:
1l
d3fa3l_
L:
1m
d3fa3m_
M:
1n
d3fa3n_
N:
1o
d3fa3o_
O:
1p
d3fa3p_
P:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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Asym.Unit (728 KB)
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