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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE HETEROTETRAMERIC COMPLEX OF GLUCD AND GLUCDRP FROM E. COLI K-12 MG1655 (EFI TARGET EFI-506058)

Authors :   T. Lukk, S. Ghasempur, H. J. Imker, J. A. Gerlt, S. K. Nair, Enzyme Funct Initiative (Efi)

Date :   05 Sep 12 (Deposition) - 12 Sep 12 (Release) - 19 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Tim-Barrel, Lyase-Lyase Complex, Structural Genomics, Enzyme Function Initiative (Efi) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Lukk, S. Ghasempur, H. J. Imker, S. K. Nair, J. A. Gerlt
Glucarate Dehydratase And Its Related Protein From Escherichia Coli Form A Heterotetrameric Complex.
To Be Published
PubMed: search

Molecule 1 - GLUCARATE DEHYDRATASE
	Chains	:	A, B
	EC Number	:	4.2.1.40
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC18
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B2787, GUDD, JW2758, YGCX
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	GDH, GLUCD

Molecule 2 - GLUCARATE DEHYDRATASE-RELATED PROTEIN
	Chains	:	C, D
	EC Number	:	4.2.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC18
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B2788, GUDX, JW2759, YGCY
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	GDH-RP, GLUCDRP

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 14)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	GOL	4	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
5	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:235 , ASN A:237 , GLU A:260 , ASP A:261 , ASN A:289	BINDING SITE FOR RESIDUE MG A 501
02	AC2	SOFTWARE	ASN A:27 , HIS A:32 , PHE A:152 , LYS A:207 , ASN A:341 , HIS A:368 , ARG A:422 , HOH A:601 , HOH A:610 , HOH A:613	BINDING SITE FOR RESIDUE SO4 A 502
03	AC3	SOFTWARE	GLY A:299 , SER A:303 , HOH A:832 , HOH A:995 , LEU B:302 , GLN B:305 , PHE B:332 , ARG D:279	BINDING SITE FOR RESIDUE GOL A 503
04	AC4	SOFTWARE	HIS A:49 , GLN A:126 , HIS A:127 , GLY A:129 , HOH A:617 , HOH A:719 , HOH A:924 , PHE B:5 , GLY D:169 , ASN D:170	BINDING SITE FOR RESIDUE PEG A 504
05	AC5	SOFTWARE	ASP B:235 , ASN B:237 , GLU B:260 , ASP B:261 , ASN B:289	BINDING SITE FOR RESIDUE MG B 501
06	AC6	SOFTWARE	ASN B:27 , HIS B:32 , PHE B:152 , LYS B:207 , ASN B:341 , HIS B:368 , ARG B:422 , HOH B:604 , HOH B:672 , HOH B:678	BINDING SITE FOR RESIDUE SO4 B 502
07	AC7	SOFTWARE	ASN C:26 , ILE C:27 , HIS C:31 , LYS C:206 , ASN C:236 , HIS C:338 , ASN C:340 , HIS C:367 , ARG C:421 , HOH C:667 , HOH C:728 , HOH C:874 , HOH C:910	BINDING SITE FOR RESIDUE CIT C 501
08	AC8	SOFTWARE	LEU A:302 , PHE A:332 , HOH A:995 , GLY B:299 , SER B:303 , ARG C:279 , HOH C:680 , HOH C:814	BINDING SITE FOR RESIDUE GOL C 502
09	AC9	SOFTWARE	ASN C:80 , HOH C:940 , ASN D:80 , LEU D:123	BINDING SITE FOR RESIDUE PEG C 503
10	BC1	SOFTWARE	ASN D:26 , ILE D:27 , HIS D:31 , TRP D:103 , PHE D:105 , PHE D:151 , LYS D:206 , ASN D:236 , HIS D:338 , ASN D:340 , HIS D:367 , ARG D:421 , HOH D:629 , HOH D:694 , HOH D:733	BINDING SITE FOR RESIDUE CIT D 501
11	BC2	SOFTWARE	GLY B:283 , PRO B:285 , ASP B:308 , ARG D:279 , GLY D:282 , PRO D:284 , ASP D:307 , HOH D:604 , HOH D:758	BINDING SITE FOR RESIDUE P6G D 502
12	BC3	SOFTWARE	HOH C:685 , THR D:317 , SER D:319 , ARG D:323 , HOH D:606 , HOH D:639	BINDING SITE FOR RESIDUE GOL D 503
13	BC4	SOFTWARE	GLN A:391 , HOH A:731 , HOH A:925 , HOH A:926 , ARG D:376 , ASP D:402 , GLU D:404 , GLN D:405 , LYS D:408	BINDING SITE FOR RESIDUE GOL D 504
14	BC5	SOFTWARE	ASN D:360	BINDING SITE FOR RESIDUE PEG D 505

(no "SS Bond" information available for 4GYP)

Asymmetric/Biological Unit

No.	Residues
1	Pro C:168	-	Gly C:169
2	Gly C:419	-	Ala C:420

(no "SAP(SNP)/Variant" information available for 4GYP)

(no "PROSITE Motif" information available for 4GYP)

(no "Exon" information available for 4GYP)

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:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4gypa1 A:3-137 D-glucarate dehydratase                                                                                                d4gypa2 A:138-446 D-glucarate dehydratase                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eee..eeee...hhhhh...........hhhhhhh.....hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh......ee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..........hhhhhh...........ee..eee...........hhhhhhhhhhhhhhh......hhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gyp A   3 SQFTTPVVTEMQVIPVAGHDSMLMNLSGAHAPFFTRNIVIIKDNSGHTGVGEIPGGEKIRKTLEDAIPLVVGKTLGEYKNVLTLVRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAMLDLLGQHLGVNVASLLGDGQQRSEVEMLGYLFFVGNRKATPLPYQSQPDDSCDWYRLRHEEAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAESIVALAQRFPQARITLDPNGAWSLNEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGHTLSLQSVDIPLADPHFWTMQGSVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPGKITAIDTHWIWQEGNQRLTKEPFEIKGGLVQVPEKPGLGVEIDMDQVMKAHELYQKHGLGARDDAMGMQYLIPGWTFDNKRPCMVR 446
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442

Chain B from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gypb1 B:4-137 D-glucarate dehydratase                                                                                               d4gypb2 B:138-446 D-glucarate dehydratase                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eee..eee....hhhhh...........hhhhhhh.....hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh......ee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..........hhhhhh...............eee...........hhhhhhhhhhhhhhh......hhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyp B   4 QFTTPVVTEMQVIPVAGHDSMLMNLSGAHAPFFTRNIVIIKDNSGHTGVGEIPGGEKIRKTLEDAIPLVVGKTLGEYKNVLTLVRNTFADRDAGGRGLQTFDLRTTIHVVTGIEAAMLDLLGQHLGVNVASLLGDGQQRSEVEMLGYLFFVGNRKATPLPYQSQPDDSCDWYRLRHEEAMTPDAVVRLAEAAYEKYGFNDFKLKGGVLAGEEEAESIVALAQRFPQARITLDPNGAWSLNEAIKIGKYLKGSLAYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGHTLSLQSVDIPLADPHFWTMQGSVRVAQMCHEFGLTWGSHSNNHFDISLAMFTHVAAAAPGKITAIDTHWIWQEGNQRLTKEPFEIKGGLVQVPEKPGLGVEIDMDQVMKAHELYQKHGLGARDDAMGMQYLIPGWTFDNKRPCMVR 446
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443

Chain C from PDB  Type:PROTEIN  Length:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gypc1 C:6-136 automated matches                                                                                    d4gypc2 C:137-446 automated matches                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eee..eee....hhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh........eee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh..........hhhhhh...........ee..eee...........hhhhhhhhhhhhhh.......hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyp C   6 SPVITDMKVIPVAGHDSMLLNIGGAHNAYFTRNIVVLTDNAGHTGIGEAPGGDVIYQTLVDAIPMVLGQEVARLNKVVQQVHKGNQELRVNAVAALEAALLDLLGKALNVPVCELLGPGKQREAITVLGYLFYIGDRTKTDLPYVENTPGNHEWYQLRHQKAMNSEAVVRLAEASQDRYGFKDFKLKGGVLPGEQEIDTVRALKKRFPDARITVDPNGAWLLDEAISLCKGLNDVLTYAEDPCGAEQGFSGREVMAEFRRATGLPVATNMIATNWREMGHAVMLNAVDIPLADPHFWTLSGAVRVAQLCDDWGLTWGCHSNNHFDISLAMFTHVGAAAPGNPTAIDTHWIWQEGDCRLTQNPLEIKNGKIAVPDAPGLGVELDWEQVQKAHEAYKRLPGGARNDAGPMQYLIPGWTFDRKRPVFGRH 446
                                    15        25        35        45        55        65        75        85     ||109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       
                                                                                                                91|                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                106

Chain D from PDB  Type:PROTEIN  Length:440
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4gypd1 D:6-136 automated matches                                                                                                  d4gypd2 D:137-445 automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eee..eee....hhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh........eee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..........hhhhhh...........ee..eee...........hhhhhhhhhhhhhhh......hhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyp D   6 SPVITDMKVIPVAGHDSMLLNIGGAHNAYFTRNIVVLTDNAGHTGIGEAPGGDVIYQTLVDAIPMVLGQEVARLNKVVQQVHKGNQAADFDTFGKGAWTFELRVNAVAALEAALLDLLGKALNVPVCELLGPGKQREAITVLGYLFYIGDRTKTDLPYVENTPGNHEWYQLRHQKAMNSEAVVRLAEASQDRYGFKDFKLKGGVLPGEQEIDTVRALKKRFPDARITVDPNGAWLLDEAISLCKGLNDVLTYAEDPCGAEQGFSGREVMAEFRRATGLPVATNMIATNWREMGHAVMLNAVDIPLADPHFWTLSGAVRVAQLCDDWGLTWGCHSNNHFDISLAMFTHVGAAAPGNPTAIDTHWIWQEGDCRLTQNPLEIKNGKIAVPDAPGLGVELDWEQVQKAHEAYKRLPGGARNDAGPMQYLIPGWTFDRKRPVFGR 445
                                    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       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445

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 '\|'

(no "CATH Domain" information available for 4GYP)

(no "Pfam Domain" information available for 4GYP)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		CIT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Gly C:419 - Ala C:420	[ RasMol ]
		Pro C:168 - Gly C:169	[ RasMol ]

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	4gyp
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	GUDX_ECOLI \| Q46915
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	4.2.1.-
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	4.2.1.40
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UniProtKB/Swiss-Prot
	GUDD_ECOLI \| P0AES2	:	1ec7 1ec8 1ec9 1ecq 1jct 1jdf 3pwg 3pwi
	GUDX_ECOLI \| Q46915	:	4il0

1ec7	E. COLI D-GLUCARATE DEHYDRATASE NATIVE ENZYME
1ec8	E. COLI D-GLUCARATE DEHYDRATASE BOUND TO PRODUCT 2,3- DIHYDROXY-5-OXO-HEXANEDIOATE
1ec9	E. COLI D-GLUCARATE DEHYDRATASE BOUND TO XYLAROHYDROXAMATE
1ecq	E. COLI D-GLUCARATE DEHYDRATASE BOUND TO 4-DEOXYGLUCARATE RELATED ID: EFI-506058 RELATED DB: TARGETTRACK

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 8)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 14)

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