3BIO - JenaLib

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Title :   CRYSTAL STRUCTURE OF OXIDOREDUCTASE (GFO/IDH/MOCA FAMILY MEMBER) FROM PORPHYROMONAS GINGIVALIS W83

Authors :   B. Nocek, R. Mulligan, S. Moy, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)

Date :   30 Nov 07 (Deposition) - 25 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Structural Genomics, Oxidoreductase, Mcsg, Psi-2, Gfo/Idh/Moca Family, Protein Structure Initiative, Midwest Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Nocek, R. Mulligan, S. Moy, A. Joachimiak
Crystal Structure Of Oxidoreductase (Gfo/Idh/Moca Family Member) From Porphyromonas Gingivalis W83.
To Be Published
PubMed: search

Molecule 1 - OXIDOREDUCTASE, GFO/IDH/MOCA FAMILY
	Atcc	:	BAA-308
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PG_0806
	Organism Scientific	:	PORPHYROMONAS GINGIVALIS
	Organism Taxid	:	242619
	Strain	:	W83

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 24)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	GOL	1	Ligand/Ion	GLYCEROL
4	MSE	20	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (4, 24)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	GOL	1	Ligand/Ion	GLYCEROL
4	MSE	20	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (4, 72)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	EPE	6	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	GOL	3	Ligand/Ion	GLYCEROL
4	MSE	60	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:16 , MSE A:154	BINDING SITE FOR RESIDUE ACT A 3001
2	AC2	SOFTWARE	ASP A:94 , GLY A:122 , TRP A:123 , ASP A:124 , PHE A:148 , SER A:153 , THR A:173 , HIS A:229 , THR A:259 , HOH A:5023 , HOH A:5105	BINDING SITE FOR RESIDUE EPE A 1001
3	AC3	SOFTWARE	ASP B:94 , GLY B:122 , TRP B:123 , ASP B:124 , PHE B:148 , MSE B:152 , SER B:153 , THR B:173 , HIS B:229 , THR B:259 , HOH B:1053 , HOH B:1086	BINDING SITE FOR RESIDUE EPE B 1001
4	AC4	SOFTWARE	HIS A:96 , ARG A:132 , PHE A:148 , LYS B:299	BINDING SITE FOR RESIDUE GOL A 5001

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

Asymmetric Unit

No.	Residues
1	Asp A:124	-	Pro A:125
2	Gly A:149	-	Pro A:150
3	Asp B:124	-	Pro B:125
4	Gly B:149	-	Pro B:150

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

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

(no "Exon" information available for 3BIO)

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:290
 aligned with Q7MW40_PORGI | Q7MW40 from UniProtKB/TrEMBL  Length:301

    Alignment length:297
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       
         Q7MW40_PORGI     5 KKIRAAIVGYGNIGRYALQALREAPDFEIAGIVRRNPAEVPFELQPFRVVSDIEQLESVDVALVCSPSREVERTALEILKKGICTADSFDIHDGILALRRSLGDAAGKSGAAAVIASGWDPGSDSVVRTLMQAIVPKGITYTNFGPGMSMGHTVAVKAIDGVKAALSMTIPLGTGVHRRMVYVELLPGHNLEEVSAAIKADEYFVHDETHVIQVDEVDALIDMGHGVRMVRKGVSGSTQNQRMSFDMEINNPALTGQVLVCAARAAMRQQPGAYTLQEIPVIDLLPGDREQWIGKLC 301
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bioA01 A:5-140,A:255-301 NAD(P)-bi       nding Rossmann-like Domain                                                                    3bioA02 A:141-254 Dihydrodipicolinate Reductase; domain 2                                                         3bioA01 A:5-140,A:255-301                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh..eeeeeee..-------......ee.hhhhh....eeee..hhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh.eeeeeeee..eehhhhhhhhhh...eeeeeeeeee.....eeeeeeeee....hhhhhhhhhhhh......eeeeee..hhhhhh..eeeeeeeeeeee..eeeeeeeeeeeeehhhhhhhhhhhhhhhhh....eeehhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bio A   5 KKIRAAIVGYGNIGRYALQALREAPDFEIAGIVRR-------ELQPFRVVSDIEQLESVDVALVCSPSREVERTALEILKKGICTADSFDIHDGILALRRSLGDAAGKSGAAAVIASGWDPGSDSVVRTLmQAIVPKGITYTNFGPGmSmGHTVAVKAIDGVKAALSmTIPLGTGVHRRmVYVELLPGHNLEEVSAAIKADEYFVHDETHVIQVDEVDALIDmGHGVRmVRKGVSGSTQNQRmSFDmEINNPALTGQVLVCAARAAmRQQPGAYTLQEIPVIDLLPGDREQWIGKLC 301
                                    14        24        34    |    -  |     54        64        74        84        94       104       114       124       134|      144       154       164       174       184       194       204       214       224  |    234       244  |   |254       264      |274       284       294       
                                                             39      47                                                                                     135-MSE          152-MSE             172-MSE     184-MSE                                    227-MSE |           247-MSE                 271-MSE                          
                                                                                                                                                                               154-MSE                                                                        233-MSE           251-MSE

Chain B from PDB  Type:PROTEIN  Length:291
 aligned with Q7MW40_PORGI | Q7MW40 from UniProtKB/TrEMBL  Length:301

    Alignment length:297
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       
         Q7MW40_PORGI     5 KKIRAAIVGYGNIGRYALQALREAPDFEIAGIVRRNPAEVPFELQPFRVVSDIEQLESVDVALVCSPSREVERTALEILKKGICTADSFDIHDGILALRRSLGDAAGKSGAAAVIASGWDPGSDSVVRTLMQAIVPKGITYTNFGPGMSMGHTVAVKAIDGVKAALSMTIPLGTGVHRRMVYVELLPGHNLEEVSAAIKADEYFVHDETHVIQVDEVDALIDMGHGVRMVRKGVSGSTQNQRMSFDMEINNPALTGQVLVCAARAAMRQQPGAYTLQEIPVIDLLPGDREQWIGKLC 301
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bioB01 B:5-140,B:255-301 NAD(P)-bindi      ng Rossmann-like Domain                                                                     3bioB02 B:141-254 Dihydrodipicolinate Reductase; domain 2                                                         3bioB01 B:5-140,B:255-301                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh..eeeeeee.....------....ee.hhhhh....eeee..hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh.eeeeeeee..eehhhhhhhhhh...eeeeeeeeee.....eeeeeeeee....hhhhhhhhhhhh......eeeeee..hhhhhh..eeeeeeeeeeee..eeeeeeeeeeeeehhhhhhhhhhhhhhhhh....eeehhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bio B   5 KKIRAAIVGYGNIGRYALQALREAPDFEIAGIVRRNPA------QPFRVVSDIEQLESVDVALVCSPSREVERTALEILKKGICTADSFDIHDGILALRRSLGDAAGKSGAAAVIASGWDPGSDSVVRTLmQAIVPKGITYTNFGPGmSmGHTVAVKAIDGVKAALSmTIPLGTGVHRRmVYVELLPGHNLEEVSAAIKADEYFVHDETHVIQVDEVDALIDmGHGVRmVRKGVSGSTQNQRmSFDmEINNPALTGQVLVCAARAAmRQQPGAYTLQEIPVIDLLPGDREQWIGKLC 301
                                    14        24        34       | -    |   54        64        74        84        94       104       114       124       134|      144       154       164       174       184       194       204       214       224  |    234       244  |   |254       264      |274       284       294       
                                                                42     49                                                                                   135-MSE          152-MSE             172-MSE     184-MSE                                    227-MSE |           247-MSE                 271-MSE                          
                                                                                                                                                                               154-MSE                                                                        233-MSE           251-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 3BIO)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q7MW40_PORGI | Q7MW40)

molecular function
	GO:0047850	diaminopimelate dehydrogenase activity	Catalysis of the reaction: meso-2,6-diaminopimelate + H(2)O + NADP(+) = L-2-amino-6-oxopimelate + H(+) + NADPH + NH(4)(+).
	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:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019877	diaminopimelate biosynthetic process	The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	GO:0009089	lysine biosynthetic process via diaminopimelate	The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Asp A:124 - Pro A:125	[ RasMol ]
		Asp B:124 - Pro B:125	[ RasMol ]
		Gly A:149 - Pro A:150	[ RasMol ]
		Gly B:149 - Pro B:150	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 24)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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