1M3S - JenaLib

Title :   CRYSTAL STRUCTURE OF YCKF FROM BACILLUS SUBTILIS

Authors :   R. Sanishvili, R. Wu, D. E. Kim, F. Collart, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   28 Jun 02 (Deposition) - 21 Jan 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Sanishvili, R. Wu, D. E. Kim, J. D. Watson, F. Collart, A. Joachimiak
Crystal Structure Of Bacillus Subtilis Yckf: Structural And Functional Evolution.
J. Struct. Biol. V. 148 98 2004
PubMed-ID: 15363790 | Reference-DOI: 10.1016/J.JSB.2004.04.006
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:181
 aligned with PHI_BACSU | P42404 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:186
                             1                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      
            PHI_BACSU     - -MKTTEYVAEILNELHNSAAYISNEEADQLADHILSSHQIFTAGAGRSGLMAKSFAMRLMHMGFNAHIVGEILTPPLAEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIGKQADLIIRMPGSPKDQSNGSYKTIQPMGSLFEQTLLLFYDAVILKLMEKKGLDSETMFTHHANLE 185
               SCOP domains d1m3sa_ A: Hypothetical protein YckF                                                                                                                                                       SCOP domains
               CATH domains 1m3sA00 A:0-185 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh...eee.............eeeee.....hhhhhhhhhhhhhh..eeeeee....hhhhhhh.eeee.......-----.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------SIS  PDB: A:29-172 UniProt: 29-172                                                                                                              ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1m3s A   0 GMKTTEYVAEILNELHNSAAYISNEEADQLADHILSSHQIFTAGAGRSGLMAKSFAMRLMHMGFNAHIVGEILTPPLAEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIGKQADLIIRMPGSPKD-----YKTIQPMGSLFEQTLLLFYDAVILKLMEKKGLDSETMFTHHANLE 185
                                     9        19        29        39        49        59        69        79        89        99       109       119       129     |   - |     149       159       169       179      
                                                                                                                                                                 135   141

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with PHI_BACSU | P42404 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:186
                             1                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      
            PHI_BACSU     - -MKTTEYVAEILNELHNSAAYISNEEADQLADHILSSHQIFTAGAGRSGLMAKSFAMRLMHMGFNAHIVGEILTPPLAEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIGKQADLIIRMPGSPKDQSNGSYKTIQPMGSLFEQTLLLFYDAVILKLMEKKGLDSETMFTHHANLE 185
               SCOP domains d1m3sb_ B: Hypothetical protein YckF                                                                                                                                                       SCOP domains
               CATH domains 1m3sB00 B:0-185 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                       CATH domains
           Pfam domains (1) --------------------------------SIS-1m3sB01 B:32-157                                                                                                          ---------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------SIS-1m3sB02 B:32-157                                                                                                          ---------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh...eee.............eeeee.....hhhhhhhhhhhhhh..eeeeee....hhhhhhh.eeee...hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh..---.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------SIS  PDB: B:29-172 UniProt: 29-172                                                                                                              ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1m3s B   0 GMKTTEYVAEILNELHNSAAYISNEEADQLADHILSSHQIFTAGAGRSGLMAKSFAMRLMHMGFNAHIVGEILTPPLAEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIGKQADLIIRMPGSPKDQSNGSYKTIQPMGSLFEQTLLLFYDAVILKLMEKKGL---TMFTHHANLE 185
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169  |   |179      
                                                                                                                                                                                                      172 176

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Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PHI_BACSU | P42404)

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:0004360	glutamine-fructose-6-phosphate transaminase (isomerizing) activity	Catalysis of the reaction: beta-D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate.
	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:0006047	UDP-N-acetylglucosamine metabolic process	The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
	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:0019647	formaldehyde assimilation via ribulose monophosphate cycle	The pathway in which formaldehyde is used as a carbon source in the ribulose monophosphate cycle. Methanotrophic bacteria produce formaldehyde from the oxidation of methane and methanol, and then assimilate it via the ribulose monophosphate cycle to form intermediates of the central metabolic routes that are subsequently used for biosynthesis of cell material. Three molecules of formaldehyde are assimilated, forming a three-carbon intermediate of central metabolism; in this pathway, all cellular carbon is assimilated at the oxidation level of formaldehyde.
	GO:0006002	fructose 6-phosphate metabolic process	The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.
	GO:0009636	response to toxic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.

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