3L8H - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF D,D-HEPTOSE 1.7-BISPHOSPHATE PHOSPHATASE FROM B. BRONCHISEPTICA COMPLEXED WITH MAGNESIUM AND PHOSPHATE

Authors :   H. Nguyen, E. Peisach, K. N. Allen

Date :   31 Dec 09 (Deposition) - 02 Feb 10 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

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

Keywords :   Had Superfamily, Gmhb, D-Glycero-D-Manno-Heptose-1, 7-Bisphosphate Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. H. Nguyen, L. Wang, H. Huang, E. Peisach, D. Dunaway-Mariano, K. N. Allen
Structural Determinants Of Substrate Recognition In The Had Superfamily Member D-Glycero-D-Manno-Heptose-1, 7-Bisphosphate Phosphatase (Gmhb) .
Biochemistry V. 49 1082 2010
PubMed-ID: 20050614 | Reference-DOI: 10.1021/BI902019Q

Molecule 1 - PUTATIVE HALOACID DEHALOGENASE-LIKE HYDROLASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3
	Expression System Strain	:	B-834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BB4091, GMHB
	Organism Common	:	ALCALIGENES BRONCHISEPTICUS
	Organism Scientific	:	BORDETELLA BRONCHISEPTICA
	Organism Taxid	:	518

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 38)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID
2	FX1	1	Ligand/Ion	BETA-D-THREO-HEXO-2,4-DIULO-2,5-FURANOSE
3	MG	5	Ligand/Ion	MAGNESIUM ION
4	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	5	Ligand/Ion	PHOSPHATE ION
6	SAR	1	Ligand/Ion	SARCOSINE
7	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	FX1	-1	Ligand/Ion	BETA-D-THREO-HEXO-2,4-DIULO-2,5-FURANOSE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	1	Ligand/Ion	PHOSPHATE ION
6	SAR	-1	Ligand/Ion	SARCOSINE
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	FMT	-1	Ligand/Ion	FORMIC ACID
2	FX1	-1	Ligand/Ion	BETA-D-THREO-HEXO-2,4-DIULO-2,5-FURANOSE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	2	Ligand/Ion	PHOSPHATE ION
6	SAR	-1	Ligand/Ion	SARCOSINE
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (3, 7)

No.	Name	Count	Type	Full Name
1	FMT	-1	Ligand/Ion	FORMIC ACID
2	FX1	1	Ligand/Ion	BETA-D-THREO-HEXO-2,4-DIULO-2,5-FURANOSE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	1	Ligand/Ion	PHOSPHATE ION
6	SAR	-1	Ligand/Ion	SARCOSINE
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (4, 8)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	FX1	-1	Ligand/Ion	BETA-D-THREO-HEXO-2,4-DIULO-2,5-FURANOSE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	1	Ligand/Ion	PHOSPHATE ION
6	SAR	1	Ligand/Ion	SARCOSINE
7	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:7 , ASP A:9 , ASP A:126 , HOH A:181 , HOH A:188 , PO4 A:2001	BINDING SITE FOR RESIDUE MG A 801
02	AC2	SOFTWARE	CYS A:89 , HIS A:91 , CYS A:97 , CYS A:99 , ARG A:100	BINDING SITE FOR RESIDUE ZN A 901
03	AC3	SOFTWARE	ASP A:7 , ARG A:8 , ASP A:9 , THR A:50 , ASN A:51 , HOH A:181 , HOH A:188 , HOH A:199 , HOH A:587 , MG A:801	BINDING SITE FOR RESIDUE PO4 A 2001
04	AC4	SOFTWARE	ASP B:7 , ASP B:9 , ASP B:126 , HOH B:186 , HOH B:194 , PO4 B:2002	BINDING SITE FOR RESIDUE MG B 802
05	AC5	SOFTWARE	SER A:53 , ARG A:57 , ARG A:100 , HOH B:347	BINDING SITE FOR RESIDUE FMT A 2007
06	AC6	SOFTWARE	CYS B:89 , HIS B:91 , CYS B:97 , CYS B:99 , ARG B:100	BINDING SITE FOR RESIDUE ZN B 902
07	AC7	SOFTWARE	ASP A:167 , HOH A:184 , HOH A:200 , HOH A:225 , HOH A:248 , HOH A:637	BINDING SITE FOR RESIDUE MG A 180
08	AC8	SOFTWARE	ASP B:7 , ARG B:8 , ASP B:9 , THR B:50 , ASN B:51 , HOH B:186 , HOH B:194 , HOH B:349 , HOH B:560 , MG B:802	BINDING SITE FOR RESIDUE PO4 B 2002
09	AC9	SOFTWARE	PHE B:19 , SER B:53 , ARG B:57 , ARG B:100 , ARG B:129 , HOH B:550 , HOH B:685 , HOH B:697	BINDING SITE FOR RESIDUE PO4 B 2005
10	BC1	SOFTWARE	ASP C:7 , ASP C:9 , ASP C:126 , HOH C:180 , HOH C:185 , PO4 C:2003	BINDING SITE FOR RESIDUE MG C 803
11	BC2	SOFTWARE	CYS C:89 , HIS C:91 , CYS C:97 , CYS C:99 , ARG C:100	BINDING SITE FOR RESIDUE ZN C 903
12	BC3	SOFTWARE	ASP C:7 , ARG C:8 , ASP C:9 , THR C:50 , ASN C:51 , HOH C:180 , HOH C:185 , HOH C:203 , HOH C:622 , MG C:803	BINDING SITE FOR RESIDUE PO4 C 2003
13	BC4	SOFTWARE	ASP D:7 , ASP D:9 , ASP D:126 , HOH D:181 , HOH D:200 , PO4 D:2004	BINDING SITE FOR RESIDUE MG D 804
14	BC5	SOFTWARE	CYS D:89 , HIS D:91 , CYS D:97 , CYS D:99 , ARG D:100	BINDING SITE FOR RESIDUE ZN D 904
15	BC6	SOFTWARE	ASP C:15 , SER C:16 , ASP C:17 , PHE C:19 , ARG C:129 , ASN C:148 , HOH C:622	BINDING SITE FOR RESIDUE FX1 C 2006
16	BC7	SOFTWARE	ASP D:7 , ARG D:8 , ASP D:9 , THR D:50 , ASN D:51 , HOH D:547 , HOH D:574 , MG D:804	BINDING SITE FOR RESIDUE PO4 D 2004
17	BC8	SOFTWARE	ASP D:15 , SER D:16 , ARG D:129 , HOH D:210	BINDING SITE FOR RESIDUE SAR D 2008
18	BC9	SOFTWARE	HOH A:280 , PRO D:30 , GLY D:31 , GLN D:34	BINDING SITE FOR RESIDUE FMT D 2009

(no "SS Bond" information available for 3L8H)

Asymmetric Unit

No.	Residues
1	Lys A:101	-	Pro A:102
2	Lys B:101	-	Pro B:102
3	Lys C:101	-	Pro C:102
4	Lys D:101	-	Pro D:102

(no "SAP(SNP)/Variant" information available for 3L8H)

(no "PROSITE Motif" information available for 3L8H)

(no "Exon" information available for 3L8H)

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:179
 aligned with GMHBB_BORBR | Q7WG29 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
          GMHBB_BORBR     1 MKLIILDRDGVVNQDSDAFVKSPDEWIALPGSLQAIARLTQADWTVVLATNQSGLARGLFDTATLNAIHDKMHRALAQMGGVVDAIFMCPHGPDDGCACRKPLPGMYRDIARRYDVDLAGVPAVGDSLRDLQAAAQAGCAPWLVQTGNGRKTLAQGGLPEGTRVCEDLAAVAEQLLQEA 179
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...............hhhhh....hhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhh.....eeeee..............hhhhhhhhhhhh......eeee.hhhhhhhhhhhh.eeeee...hhhhhhhhh.....eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l8h A   1 mKLIILDRDGVVNQDSDAFVKSPDEWIALPGSLQAIARLTQADWTVVLATNQSGLARGLFDTATLNAIHDKmHRALAQmGGVVDAIFmCPHGPDDGCACRKPLPGmYRDIARRYDVDLAGVPAVGDSLRDLQAAAQAGCAPWLVQTGNGRKTLAQGGLPEGTRVCEDLAAVAEQLLQEA 179
                            |       10        20        30        40        50        60        70 |      80       |90       100     | 110       120       130       140       150       160       170         
                            |                                                                     72-MSE 79-MSE   88-MSE           106-MSE                                                                     
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with GMHBB_BORBR | Q7WG29 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
          GMHBB_BORBR     1 MKLIILDRDGVVNQDSDAFVKSPDEWIALPGSLQAIARLTQADWTVVLATNQSGLARGLFDTATLNAIHDKMHRALAQMGGVVDAIFMCPHGPDDGCACRKPLPGMYRDIARRYDVDLAGVPAVGDSLRDLQAAAQAGCAPWLVQTGNGRKTLAQGGLPEGTRVCEDLAAVAEQLLQEA 179
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...............hhhhh....hhhhhhhhhhhh.eeeeeeee.........hhhhhhhhhhhhhhhhhh......eeeee..............hhhhhhhhhhhh......eeee.hhhhhhhhhhhh.eeeee...hhhhhhhhh.....eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l8h B   1 mKLIILDRDGVVNQDSDAFVKSPDEWIALPGSLQAIARLTQADWTVVLATNQSGLARGLFDTATLNAIHDKmHRALAQmGGVVDAIFmCPHGPDDGCACRKPLPGmYRDIARRYDVDLAGVPAVGDSLRDLQAAAQAGCAPWLVQTGNGRKTLAQGGLPEGTRVCEDLAAVAEQLLQEA 179
                            |       10        20        30        40        50        60        70 |      80       |90       100     | 110       120       130       140       150       160       170         
                            1-MSE                                                                 72-MSE 79-MSE   88-MSE           106-MSE

Chain C from PDB  Type:PROTEIN  Length:179
 aligned with GMHBB_BORBR | Q7WG29 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
          GMHBB_BORBR     1 MKLIILDRDGVVNQDSDAFVKSPDEWIALPGSLQAIARLTQADWTVVLATNQSGLARGLFDTATLNAIHDKMHRALAQMGGVVDAIFMCPHGPDDGCACRKPLPGMYRDIARRYDVDLAGVPAVGDSLRDLQAAAQAGCAPWLVQTGNGRKTLAQGGLPEGTRVCEDLAAVAEQLLQEA 179
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...............hhhhh....hhhhhhhhhhhh.eeeeeeee.........hhhhhhhhhhhhhhhhhh......eeeee..............hhhhhhhhhhhh......eeee.hhhhhhhhhhhh.eeeee...hhhhhhhhh.....eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l8h C   1 mKLIILDRDGVVNQDSDAFVKSPDEWIALPGSLQAIARLTQADWTVVLATNQSGLARGLFDTATLNAIHDKmHRALAQmGGVVDAIFmCPHGPDDGCACRKPLPGmYRDIARRYDVDLAGVPAVGDSLRDLQAAAQAGCAPWLVQTGNGRKTLAQGGLPEGTRVCEDLAAVAEQLLQEA 179
                            |       10        20        30        40        50        60        70 |      80       |90       100     | 110       120       130       140       150       160       170         
                            1-MSE                                                                 72-MSE 79-MSE   88-MSE           106-MSE

Chain D from PDB  Type:PROTEIN  Length:179
 aligned with GMHBB_BORBR | Q7WG29 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
          GMHBB_BORBR     1 MKLIILDRDGVVNQDSDAFVKSPDEWIALPGSLQAIARLTQADWTVVLATNQSGLARGLFDTATLNAIHDKMHRALAQMGGVVDAIFMCPHGPDDGCACRKPLPGMYRDIARRYDVDLAGVPAVGDSLRDLQAAAQAGCAPWLVQTGNGRKTLAQGGLPEGTRVCEDLAAVAEQLLQEA 179
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...............hhhhh....hhhhhhhhhhhh.eeeeeeee.........hhhhhhhhhhhhhhhhhh......eeeee..............hhhhhhhhhhhh......eeee.hhhhhhhhhhhh.eeeee...hhhhhhhhh.....eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l8h D   1 mKLIILDRDGVVNQDSDAFVKSPDEWIALPGSLQAIARLTQADWTVVLATNQSGLARGLFDTATLNAIHDKmHRALAQmGGVVDAIFmCPHGPDDGCACRKPLPGmYRDIARRYDVDLAGVPAVGDSLRDLQAAAQAGCAPWLVQTGNGRKTLAQGGLPEGTRVCEDLAAVAEQLLQEA 179
                            |       10        20        30        40        50        60        70 |      80       |90       100     | 110       120       130       140       150       160       170         
                            1-MSE                                                                 72-MSE 79-MSE   88-MSE           106-MSE

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 "SCOP Domain" information available for 3L8H)

(no "CATH Domain" information available for 3L8H)

(no "Pfam Domain" information available for 3L8H)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GMHBB_BORBR | Q7WG29)

molecular function
	GO:0034200	D,D-heptose 1,7-bisphosphate phosphatase activity	Catalysis of the reaction: D-beta-D-heptose 1,7-bisphosphate + H2O = D-beta-D-heptose 1-phosphate + phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0097171	ADP-L-glycero-beta-D-manno-heptose biosynthetic process	The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0009244	lipopolysaccharide core region biosynthetic process	The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:101 - Pro A:102	[ RasMol ]
		Lys B:101 - Pro B:102	[ RasMol ]
		Lys C:101 - Pro C:102	[ RasMol ]
		Lys D:101 - Pro D:102	[ RasMol ]

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	3l8h
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(no "Entries Sharing at Least One Protein Chain" available for 3L8H)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 38)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (11, 11)

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