3G68 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOSUGAR ISOMERASE (CD3275) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.80 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   06 Feb 09 (Deposition) - 24 Feb 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Putative Phosphosugar Isomerase, Sis Domain, Double-Sis Domain Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Double-Sis Domain Protein (Yp_001089791. 1) From Clostridium Difficile 630 At 1. 80 A Resolution
To Be Published
PubMed: search

Molecule 1 - PUTATIVE PHOSPHOSUGAR ISOMERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CD3275, YP_001089791.1
	Organism Scientific	:	CLOSTRIDIUM DIFFICILE
	Organism Taxid	:	272563
	Strain	:	630

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 30)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	22	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 60)

No.	Name	Count	Type	Full Name
1	CIT	4	Ligand/Ion	CITRIC ACID
2	EDO	12	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	44	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 60)

No.	Name	Count	Type	Full Name
1	CIT	4	Ligand/Ion	CITRIC ACID
2	EDO	12	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	44	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:41 , THR A:43 , SER A:44 , SER A:89 , GLN A:90 , GLY A:91 , SER A:94 , HIS A:247 , HOH A:363 , HOH A:463 , HOH A:493 , HOH A:547 , HOH A:572 , HOH A:655 , HOH A:656 , HOH A:657	BINDING SITE FOR RESIDUE CIT A 401
2	AC2	SOFTWARE	TYR A:54 , ASN A:57 , LEU A:58 , GLU A:175	BINDING SITE FOR RESIDUE EDO A 352
3	AC3	SOFTWARE	THR A:2 , GLN A:4 , ASP A:5 , LYS B:191	BINDING SITE FOR RESIDUE EDO A 353
4	AC4	SOFTWARE	ASP A:79 , ASN A:80 , GLU A:81 , ASN A:254 , SER A:255 , HOH A:521	BINDING SITE FOR RESIDUE EDO A 354
5	AC5	SOFTWARE	SER B:41 , THR B:43 , SER B:44 , SER B:89 , GLN B:90 , GLY B:91 , SER B:94 , HIS B:247 , HOH B:521 , HOH B:551 , HOH B:555 , HOH B:562	BINDING SITE FOR RESIDUE CIT B 401
6	AC6	SOFTWARE	GLU B:209 , PRO B:236 , HOH B:510 , HOH B:559 , HOH B:603	BINDING SITE FOR RESIDUE EDO B 352
7	AC7	SOFTWARE	LEU B:192 , ILE B:300 , ASP B:301 , HOH B:561	BINDING SITE FOR RESIDUE EDO B 353
8	AC8	SOFTWARE	SER A:23 , SER B:168 , SER B:169 , GLU B:170 , HOH B:611	BINDING SITE FOR RESIDUE EDO B 354

(no "SS Bond" information available for 3G68)

(no "Cis Peptide Bond" information available for 3G68)

(no "SAP(SNP)/Variant" information available for 3G68)

(no "PROSITE Motif" information available for 3G68)

(no "Exon" information available for 3G68)

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:345
 aligned with Q180C0_PEPD6 | Q180C0 from UniProtKB/TrEMBL  Length:351

    Alignment length:345
                             1                                                                                                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     
         Q180C0_PEPD6     - -MTIQDYMLETPVRMREIISNADSLFNEVKRTNLKKIIITGSGTSYHSGVQVQPYLQNLLDIDVVKMYPFMITEDTFKFDNENTLVVGVSQGGSSYSTYNAMKLAEDKGCKIASMAGCKNALIDEISDYILTVNCGEEKSGAKTKGYYCTKLNLMLLGLQIAREKGIISSEKYNEEINKILDAINRFEAVYKLSKQWIERNKEKLVNSKEIRIIGHSDIYGDTLEAALKLLETMRIPVTGYEFEEFIHGIYNAINSDSTIFILDTGKEPRVTKMIDVLSGWTENVFAIGRDVTENDKNLKIDITDNPYYQTFNFIVPIQLICGEIPTLRGVDPSVPKDTRFHMKL 344
               SCOP domains d3g68a_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeee.hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh..eeeeee....hhhhhhh.ee.............hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhh....eeeee.........ee.......hhhhhh.hhhhhhhhhhhhhhhh.........hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g68 A   0 GmTIQDYmLETPVRmREIISNADSLFNEVKRTNLKKIIITGSGTSYHSGVQVQPYLQNLLDIDVVKmYPFmITEDTFKFDNENTLVVGVSQGGSSYSTYNAmKLAEDKGCKIASmAGCKNALIDEISDYILTVNCGEEKSGAKTKGYYCTKLNLmLLGLQIAREKGIISSEKYNEEINKILDAINRFEAVYKLSKQWIERNKEKLVNSKEIRIIGHSDIYGDTLEAALKLLETmRIPVTGYEFEEFIHGIYNAINSDSTIFILDTGKEPRVTKmIDVLSGWTENVFAIGRDVTENDKNLKIDITDNPYYQTFNFIVPIQLICGEIPTLRGVDPSVPKDTRFHmKL 344
                             |     | 9    |   19        29        39        49        59      | 69|       79        89        99 |     109    |  119       129       139       149    |  159       169       179       189       199       209       219       229   |   239       249       259       269   |   279       289       299       309       319       329       339  |  
                             |     7-MSE 14-MSE                                              66-MSE                            101-MSE      114-MSE                                 154-MSE                                                                        233-MSE                                 273-MSE                                                              342-MSE
                             1-MSE                                                               70-MSE

Chain B from PDB  Type:PROTEIN  Length:351
 aligned with Q180C0_PEPD6 | Q180C0 from UniProtKB/TrEMBL  Length:351

    Alignment length:351
                             1                                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       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 
         Q180C0_PEPD6     - -MTIQDYMLETPVRMREIISNADSLFNEVKRTNLKKIIITGSGTSYHSGVQVQPYLQNLLDIDVVKMYPFMITEDTFKFDNENTLVVGVSQGGSSYSTYNAMKLAEDKGCKIASMAGCKNALIDEISDYILTVNCGEEKSGAKTKGYYCTKLNLMLLGLQIAREKGIISSEKYNEEINKILDAINRFEAVYKLSKQWIERNKEKLVNSKEIRIIGHSDIYGDTLEAALKLLETMRIPVTGYEFEEFIHGIYNAINSDSTIFILDTGKEPRVTKMIDVLSGWTENVFAIGRDVTENDKNLKIDITDNPYYQTFNFIVPIQLICGEIPTLRGVDPSVPKDTRFHMKLGSKKLN 350
               SCOP domains d3g68b_ B: automated matches                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeee.hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh..eeeeee....hhhhhhh.ee.............hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhh...eeeeee.........ee.......hhhhhh.hhhhhhhhhhhhhhh..........hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g68 B   0 GmTIQDYmLETPVRmREIISNADSLFNEVKRTNLKKIIITGSGTSYHSGVQVQPYLQNLLDIDVVKmYPFmITEDTFKFDNENTLVVGVSQGGSSYSTYNAmKLAEDKGCKIASmAGCKNALIDEISDYILTVNCGEEKSGAKTKGYYCTKLNLmLLGLQIAREKGIISSEKYNEEINKILDAINRFEAVYKLSKQWIERNKEKLVNSKEIRIIGHSDIYGDTLEAALKLLETmRIPVTGYEFEEFIHGIYNAINSDSTIFILDTGKEPRVTKmIDVLSGWTENVFAIGRDVTENDKNLKIDITDNPYYQTFNFIVPIQLICGEIPTLRGVDPSVPKDTRFHmKLGSKKLN 350
                             |     | 9    |   19        29        39        49        59      | 69|       79        89        99 |     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 
                             |     7-MSE 14-MSE                                              66-MSE                            101-MSE      114-MSE                                 154-MSE                                                                        233-MSE                                 273-MSE                                                              342-MSE    
                             1-MSE                                                               70-MSE

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(

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

Fold: SIS domain (85)

Superfamily: SIS domain (85)

Family: automated matches (22)

Protein domain: automated matches (22)

Clostridium difficile [TaxId: 272563] (1)

1a	d3g68a_	A:
1b	d3g68b_	B:

(no "CATH Domain" information available for 3G68)

(no "Pfam Domain" information available for 3G68)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q180C0_PEPD6 | Q180C0)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
	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.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3g68)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 30)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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