4MMW - JenaLib

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Title :   CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS COMPLEXED WITH MAGNESIUM, L-XYLAROHYDROXAMATE AND L-LYXAROHYDROXAMATE

Authors :   A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo

Date :   09 Sep 13 (Deposition) - 18 Sep 13 (Release) - 18 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (1x),B (1x)
Biol. Unit 3: A,B  (4x)

Keywords :   Enolase Fold, D-Glucarate Dehydratase, L-Xylarohydroxamate, L- Lyxarohydroxamate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo
Crystal Structure Of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed With Magnesium, L-Xylarohydroxamate And L-Lyxarohydroxamate
To Be Published
PubMed: search

Molecule 1 - ISOMERASE/LACTONIZING ENZYME
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ATU3453
	Organism Common	:	AGROBACTERIUM TUMEFACIENS
	Organism Scientific	:	AGROBACTERIUM FABRUM
	Organism Taxid	:	176299
	Strain	:	C58 / ATCC 33970

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A (1x)	B (1x)
Biological Unit 3 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 21)

No.	Name	Count	Type	Full Name
1	CL	10	Ligand/Ion	CHLORIDE ION
2	LLH	2	Ligand/Ion	(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID
3	MG	6	Ligand/Ion	MAGNESIUM ION
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
5	XYH	2	Ligand/Ion	XYLAROHYDROXAMATE

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	LLH	2	Ligand/Ion	(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
5	XYH	2	Ligand/Ion	XYLAROHYDROXAMATE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	LLH	1	Ligand/Ion	(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
5	XYH	1	Ligand/Ion	XYLAROHYDROXAMATE

Biological Unit 3 (3, 20)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	LLH	8	Ligand/Ion	(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL
5	XYH	8	Ligand/Ion	XYLAROHYDROXAMATE

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:335 , HOH A:669 , HOH A:698 , HOH A:854 , HOH A:857 , HOH A:859	BINDING SITE FOR RESIDUE MG A 401
02	AC2	SOFTWARE	ASP A:206 , GLU A:232 , GLU A:258 , XYH A:404 , LLH A:405 , HOH A:794	BINDING SITE FOR RESIDUE MG A 402
03	AC3	SOFTWARE	SER A:247 , LEU A:250 , HOH A:795 , HOH A:796 , HOH A:797 , HOH A:798	BINDING SITE FOR RESIDUE MG A 403
04	AC4	SOFTWARE	HIS A:24 , CYS A:139 , LYS A:169 , HIS A:171 , ASP A:206 , HIS A:209 , GLU A:232 , GLU A:258 , ARG A:280 , HIS A:309 , GLU A:329 , MG A:402 , HOH A:543 , HOH A:548 , HOH A:794 , HOH A:851 , ARG B:90	BINDING SITE FOR RESIDUE XYH A 404
05	AC5	SOFTWARE	HIS A:24 , LYS A:169 , HIS A:171 , ASP A:206 , HIS A:209 , GLU A:232 , GLU A:258 , ARG A:280 , HIS A:309 , GLU A:329 , MG A:402 , HOH A:543 , HOH A:548 , HOH A:794 , HOH A:840 , HOH A:851 , ARG B:90	BINDING SITE FOR RESIDUE LLH A 405
06	AC6	SOFTWARE	ARG A:163 , ARG A:330 , ASP A:340 , LEU A:349 , PRO A:352 , MET A:353	BINDING SITE FOR RESIDUE CL A 406
07	AC7	SOFTWARE	ARG A:128 , VAL A:131 , LEU A:132 , HOH A:545	BINDING SITE FOR RESIDUE CL A 407
08	AC8	SOFTWARE	LYS A:347 , PHE A:373 , THR A:374	BINDING SITE FOR RESIDUE CL A 408
09	AC9	SOFTWARE	MET A:1 , ASP A:74	BINDING SITE FOR RESIDUE CL A 409
10	BC1	SOFTWARE	MET A:1 , ARG A:76	BINDING SITE FOR RESIDUE CL A 410
11	BC2	SOFTWARE	GLN A:238 , ALA A:261 , HOH A:869 , GLN B:238 , ALA B:261 , GLY B:262 , HOH B:644	BINDING SITE FOR RESIDUE PGE A 411
12	BC3	SOFTWARE	GLU A:338 , PRO B:335 , HOH B:676 , HOH B:804 , HOH B:842 , HOH B:856 , HOH B:857	BINDING SITE FOR RESIDUE MG B 401
13	BC4	SOFTWARE	ASP B:206 , GLU B:232 , GLU B:258 , XYH B:404 , LLH B:405 , HOH B:786	BINDING SITE FOR RESIDUE MG B 402
14	BC5	SOFTWARE	SER B:247 , LEU B:250 , HOH B:787 , HOH B:788 , HOH B:789 , HOH B:790	BINDING SITE FOR RESIDUE MG B 403
15	BC6	SOFTWARE	ARG A:90 , HIS B:24 , LYS B:169 , HIS B:171 , ASP B:206 , HIS B:209 , GLU B:232 , GLU B:258 , ARG B:280 , HIS B:309 , GLU B:329 , MG B:402 , HOH B:545 , HOH B:568 , HOH B:786 , HOH B:855	BINDING SITE FOR RESIDUE XYH B 404
16	BC7	SOFTWARE	ARG A:90 , HIS B:24 , LYS B:169 , HIS B:171 , ASP B:206 , HIS B:209 , GLU B:232 , GLU B:258 , ARG B:280 , HIS B:309 , GLU B:329 , MG B:402 , HOH B:545 , HOH B:568 , HOH B:786 , HOH B:835 , HOH B:855	BINDING SITE FOR RESIDUE LLH B 405
17	BC8	SOFTWARE	ARG B:163 , ARG B:330 , LEU B:349 , MET B:353	BINDING SITE FOR RESIDUE CL B 406
18	BC9	SOFTWARE	HOH A:676 , PRO B:59 , HIS B:60 , HOH B:841	BINDING SITE FOR RESIDUE CL B 407
19	CC1	SOFTWARE	ARG B:128 , VAL B:131 , LEU B:132	BINDING SITE FOR RESIDUE CL B 408
20	CC2	SOFTWARE	MET B:1 , ASP B:74	BINDING SITE FOR RESIDUE CL B 409
21	CC3	SOFTWARE	MET B:1 , ARG B:76	BINDING SITE FOR RESIDUE CL B 410

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

Asymmetric Unit

No.	Residues
1	Pro A:175	-	Pro A:176
2	Ala A:180	-	Pro A:181
3	Gly A:256	-	Pro A:257
4	Gly A:331	-	Leu A:332
5	Pro B:175	-	Pro B:176
6	Ala B:180	-	Pro B:181
7	Gly B:256	-	Pro B:257
8	Gly B:331	-	Leu B:332

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

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

(no "Exon" information available for 4MMW)

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:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4mmwa1 A:1-126 automated matches                                                                                             d4mmwa2 A:127-381 automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eeeeeeee...........hhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh...ee......hhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhh......eeeeee....hhhhh...............eee...........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mmw A   1 MIITDVEVRVFRTTTRRHSDSAGHAHPGPAHQVEQAMLTVRTEDGQEGHSFTAPEIVRPHVIEKFVKKVLIGEDHRDRERLWQDLAHWQRGSAAQLTDRTLAVVDCALWDLAGRSLGQPVYKLIGGYRDKVLAYGSIMCGDELEGGLATPEDYGRFAETLVKRGYKGIKLHTWMPPVSWAPDVKMDLKACAAVREAVGPDIRLMIDAFHWYSRTDALALGRGLEKLGFDWIEEPMDEQSLSSYKWLSDNLDIPVVGPESAAGKHWHRAEWIKAGACDILRTGVNDVGGITPALKTMHLAEAFGMECEVHGNTAMNLHVVAATKNCRWYERGLLHPFLEYDDGHDYLKSLSDPMDRDGFVHVPDRPGLGEDIDFTFIDNNRV 381
                                    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       320       330       340       350       360       370       380

Chain B from PDB  Type:PROTEIN  Length:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4mmwb1 B:1-126 automated matches                                                                                             d4mmwb2 B:127-381 automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eeeeeeee...........hhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhh......eeeeee....hhhhh...............eee...........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mmw B   1 MIITDVEVRVFRTTTRRHSDSAGHAHPGPAHQVEQAMLTVRTEDGQEGHSFTAPEIVRPHVIEKFVKKVLIGEDHRDRERLWQDLAHWQRGSAAQLTDRTLAVVDCALWDLAGRSLGQPVYKLIGGYRDKVLAYGSIMCGDELEGGLATPEDYGRFAETLVKRGYKGIKLHTWMPPVSWAPDVKMDLKACAAVREAVGPDIRLMIDAFHWYSRTDALALGRGLEKLGFDWIEEPMDEQSLSSYKWLSDNLDIPVVGPESAAGKHWHRAEWIKAGACDILRTGVNDVGGITPALKTMHLAEAFGMECEVHGNTAMNLHVVAATKNCRWYERGLLHPFLEYDDGHDYLKSLSDPMDRDGFVHVPDRPGLGEDIDFTFIDNNRV 381
                                    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       320       330       340       350       360       370       380

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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 '\|'

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

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

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	Cis Peptide Bonds
		Ala A:180 - Pro A:181	[ RasMol ]
		Ala B:180 - Pro B:181	[ RasMol ]
		Gly A:256 - Pro A:257	[ RasMol ]
		Gly A:331 - Leu A:332	[ RasMol ]
		Gly B:256 - Pro B:257	[ RasMol ]
		Gly B:331 - Leu B:332	[ RasMol ]
		Pro A:175 - Pro A:176	[ RasMol ]
		Pro B:175 - Pro B:176	[ RasMol ]

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	Q7CSI0_AGRFC \| Q7CSI0	:	1rvk 4hcd 4hch 4hcl

1rvk	THE SAME PROTEIN UNCOMPLEXED

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 21)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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