3AW9 - JenaLib

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Title :   STRUCTURE OF UDP-GALACTOSE 4-EPIMERASE MUTANT

Authors :   H. Sakuraba, T. Kawai, K. Yoneda, T. Ohshima

Date :   15 Mar 11 (Deposition) - 29 Feb 12 (Release) - 18 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Rossmann Fold, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Sakuraba, T. Kawai, K. Yoneda, T. Ohshima
Structure Of Udp-Galactose 4-Epimerase Mutant
To Be Published
PubMed: search

Molecule 1 - NAD-DEPENDENT EPIMERASE/DEHYDRATASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PCAL_0885
	Mutation	:	YES
	Organism Scientific	:	PYROBACULUM CALIDIFONTIS
	Organism Taxid	:	410359
	Strain	:	JCM 11548 / VA1

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	GDU	3	Ligand/Ion	GALACTOSE-URIDINE-5'-DIPHOSPHATE
2	NAD	3	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	GDU	2	Ligand/Ion	GALACTOSE-URIDINE-5'-DIPHOSPHATE
2	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	GDU	2	Ligand/Ion	GALACTOSE-URIDINE-5'-DIPHOSPHATE
2	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:69 , VAL A:71 , SER A:109 , SER A:110 , TYR A:133 , TYR A:160 , ASN A:162 , HIS A:170 , ASP A:175 , PHE A:176 , VAL A:189 , LEU A:190 , GLN A:195 , LYS A:197 , TYR A:199 , VAL A:236 , GLY A:264 , ASP A:268 , MET A:272 , HOH A:368 , HOH A:394 , NAD A:901	BINDING SITE FOR RESIDUE GDU A 801
2	AC2	SOFTWARE	GLY A:7 , GLY A:10 , PHE A:11 , ILE A:12 , ASP A:31 , ILE A:32 , ARG A:46 , ASP A:47 , LEU A:48 , LYS A:49 , PHE A:65 , ALA A:66 , ALA A:67 , GLU A:84 , ALA A:107 , SER A:108 , TYR A:133 , LYS A:137 , TYR A:160 , ALA A:161 , ASN A:162 , VAL A:163 , HIS A:170 , HOH A:321 , HOH A:328 , HOH A:335 , HOH A:339 , HOH A:386 , GDU A:801	BINDING SITE FOR RESIDUE NAD A 901
3	AC3	SOFTWARE	HOH B:53 , HOH B:123 , HOH B:253 , PRO B:1069 , GLU B:1070 , VAL B:1071 , SER B:1109 , SER B:1110 , THR B:1111 , TYR B:1133 , TYR B:1160 , ASN B:1162 , VAL B:1172 , ASP B:1175 , VAL B:1189 , LEU B:1190 , GLN B:1195 , LYS B:1197 , TYR B:1199 , VAL B:1236 , TRP B:1265 , ASP B:1268 , VAL B:1269 , MET B:1272 , NAD B:1901	BINDING SITE FOR RESIDUE GDU B 1801
4	AC4	SOFTWARE	HOH B:28 , HOH B:31 , HOH B:41 , HOH B:42 , HOH B:56 , HOH B:101 , HOH B:144 , HOH B:159 , HOH B:193 , GLY B:1007 , GLY B:1010 , PHE B:1011 , ILE B:1012 , ASP B:1031 , ILE B:1032 , ARG B:1046 , ASP B:1047 , LEU B:1048 , LYS B:1049 , PHE B:1065 , ALA B:1066 , ALA B:1067 , PRO B:1069 , GLU B:1084 , ALA B:1107 , SER B:1108 , TYR B:1133 , LYS B:1137 , TYR B:1160 , ALA B:1161 , ASN B:1162 , VAL B:1163 , HIS B:1170 , GDU B:1801	BINDING SITE FOR RESIDUE NAD B 1901
5	AC5	SOFTWARE	HOH C:70 , HOH C:114 , PRO C:2069 , VAL C:2071 , ARG C:2072 , SER C:2109 , SER C:2110 , THR C:2111 , TYR C:2133 , TYR C:2160 , ASN C:2162 , VAL C:2172 , ASP C:2175 , LEU C:2190 , GLN C:2195 , LYS C:2197 , TYR C:2199 , VAL C:2236 , TRP C:2265 , ASP C:2268 , NAD C:2901	BINDING SITE FOR RESIDUE GDU C 2801
6	AC6	SOFTWARE	HOH C:9 , HOH C:13 , HOH C:19 , HOH C:21 , HOH C:94 , HOH C:112 , HOH C:135 , GLY C:2007 , GLY C:2010 , PHE C:2011 , ILE C:2012 , ASP C:2031 , ILE C:2032 , ARG C:2046 , ASP C:2047 , LEU C:2048 , PHE C:2065 , ALA C:2066 , ALA C:2067 , PRO C:2069 , GLU C:2084 , ALA C:2107 , SER C:2108 , TYR C:2133 , LYS C:2137 , TYR C:2160 , ALA C:2161 , ASN C:2162 , VAL C:2163 , HIS C:2170 , GDU C:2801	BINDING SITE FOR RESIDUE NAD C 2901

Asymmetric Unit

No.	Residues
1	A:144	-	A:155
2	B:1144	-	B:1155
3	C:2144	-	C:2155

Asymmetric Unit

No.	Residues
1	Ile A:119	-	Pro A:120
2	Ile B:1119	-	Pro B:1120
3	Ile C:2119	-	Pro C:2120

(no "SAP(SNP)/Variant" information available for 3AW9)

(no "PROSITE Motif" information available for 3AW9)

(no "Exon" information available for 3AW9)

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:304
 aligned with A3MUJ4_PYRCJ | A3MUJ4 from UniProtKB/TrEMBL  Length:312

    Alignment length:310
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
        A3MUJ4_PYRCJ      1 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDNLSSGRREFVNPSAELHVRDLKDYSWGAGIKGDVVFHFAANPEVRLSTTEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTVYGDADVIPTPEEEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYANVVGPRLRHGVIYDFIMKLRRNPNVLEVLGDGTQRKSYLYVRDAVEATLAAWKKFEEMDAPFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLVPSTPDGRGWPGDVKYMTLAVTKLMKLTGWRPTMTSAEAVKKTAEDLAKEL  310
               SCOP domains d3aw9a_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee.......----...eeee....hhhhhh.....eeee........--..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee......hhhhhhhhhhhhh..eeeee.....ee.eeehhhhhhhhhhhhhhhhh....eeeeee.....eehhhhhhhhhhhhh...eeeee..............ee...hhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3aw9 A    1 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDIVQRDTG----GSAELHVRDLKDYSWGAGIKGDVVFHFAANPEVR--TTEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTVYGDADVIPTPEEEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYANVVGPRLRHGVIYDFIMKLRRNPNVLEVLGDGTQRKSYLYVRDAVEATLAAWKKFEEMDAPFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLVPSTPDGRGWPGDVKYMTLAVTKLMKLTGWRPTMTSAEAVKKTAEDLAKEL  306
                                    10        20        30       | -  |     46        56        66     |  76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306
                                                                38   39                               72 75

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with A3MUJ4_PYRCJ | A3MUJ4 from UniProtKB/TrEMBL  Length:312

    Alignment length:310
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
        A3MUJ4_PYRCJ      1 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDNLSSGRREFVNPSAELHVRDLKDYSWGAGIKGDVVFHFAANPEVRLSTTEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTVYGDADVIPTPEEEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYANVVGPRLRHGVIYDFIMKLRRNPNVLEVLGDGTQRKSYLYVRDAVEATLAAWKKFEEMDAPFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLVPSTPDGRGWPGDVKYMTLAVTKLMKLTGWRPTMTSAEAVKKTAEDLAKEL  310
               SCOP domains d3aw9b_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee..---...-----.eeee...............eeee........--..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee......hhhhhhhhhhhhh..eeeee.....ee.eeehhhhhhhhhhhhhhhh.....eeeeee.....eehhhhhhhhhhhh....eeeee...................hhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3aw9 B 1001 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDIV---QRD-----AELHVRDLKDYSWGAGIKGDVVFHFAANPEVR--TTEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTVYGDADVIPTPEEEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYANVVGPRLRHGVIYDFIMKLRRNPNVLEVLGDGTQRKSYLYVRDAVEATLAAWKKFEEMDAPFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLVPSTPDGRGWPGDVKYMTLAVTKLMKLTGWRPTMTSAEAVKKTAEDLAKEL 1306
                                  1010      1020      1030  |   | |-    | 1046      1056      1066     |1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306
                                                         1033   | |  1041                           1072  |                                                                                                                                                                                                                                       
                                                             1034 |                                    1075                                                                                                                                                                                                                                       
                                                               1036

Chain C from PDB  Type:PROTEIN  Length:299
 aligned with A3MUJ4_PYRCJ | A3MUJ4 from UniProtKB/TrEMBL  Length:312

    Alignment length:310
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
        A3MUJ4_PYRCJ      1 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDNLSSGRREFVNPSAELHVRDLKDYSWGAGIKGDVVFHFAANPEVRLSTTEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTVYGDADVIPTPEEEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYANVVGPRLRHGVIYDFIMKLRRNPNVLEVLGDGTQRKSYLYVRDAVEATLAAWKKFEEMDAPFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLVPSTPDGRGWPGDVKYMTLAVTKLMKLTGWRPTMTSAEAVKKTAEDLAKEL  310
               SCOP domains d3aw9c_ C: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh.eeeeee..---...-----.eeee...............eeee........---.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee......hhhhhhhhhhhhh..eeeee.....ee.eeehhhhhhhhhhhhhhhh.....eeeeee.....eehhhhhhhhhhhhh...eeeee..............ee...hhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3aw9 C 2001 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDIV---QRD-----AELHVRDLKDYSWGAGIKGDVVFHFAANPEVR---TEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTVYGDADVIPTPEEEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYANVVGPRLRHGVIYDFIMKLRRNPNVLEVLGDGTQRKSYLYVRDAVEATLAAWKKFEEMDAPFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLVPSTPDGRGWPGDVKYMTLAVTKLMKLTGWRPTMTSAEAVKKTAEDLAKEL 2306
                                  2010      2020      2030  |   | |-    | 2046      2056      2066     |2076      2086      2096      2106      2116      2126      2136      2146      2156      2166      2176      2186      2196      2206      2216      2226      2236      2246      2256      2266      2276      2286      2296      2306
                                                         2033   | |  2041                           2072   |                                                                                                                                                                                                                                      
                                                             2034 |                                     2076                                                                                                                                                                                                                                      
                                                               2036

Legend:		→ Mismatch	(orange background)
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	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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Pyrobaculum calidifontis [TaxId: 181486] (1)

1a	d3aw9a_	A:
1b	d3aw9b_	B:
1c	d3aw9c_	C:

(no "CATH Domain" information available for 3AW9)

(no "Pfam Domain" information available for 3AW9)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (A3MUJ4_PYRCJ | A3MUJ4)

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:0050662	coenzyme binding	Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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	Cis Peptide Bonds
		Ile A:119 - Pro A:120	[ RasMol ]
		Ile B:1119 - Pro B:1120	[ RasMol ]
		Ile C:2119 - Pro C:2120	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3AW9)

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

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