2F2G - JenaLib

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Title :   X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT3G16990

Authors :   G. W. Wesenberg, D. W. Smith, G. N. Phillips Jr. , K. A. Johnson, E. Bitto C. A. Bingman, Center For Eukaryotic Structural Genomics (Cesg

Date :   16 Nov 05 (Deposition) - 13 Dec 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Tena_thi-4 Domain, Tena/Thi-4/Pqqc Family, At3G16990, Structural Genomics, Protein Structure Initiative, Psi, Cesg, Center Foreukaryotic Structural Genomics, Center For Eukaryotic Structural Genomics, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. G. Blommel, D. W. Smith, C. A. Bingman, D. H. Dyer, I. Rayment, H. M. Holden, B. G. Fox, G. N. Phillips Jr.
Crystal Structure Of Gene Locus At3G16990 From Arabidopsis Thaliana
Proteins V. 57 221 2004
PubMed-ID: 15326608 | Reference-DOI: 10.1002/PROT.20213

Molecule 1 - SEED MATURATION PROTEIN PM36 HOMOLOG
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP13
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AT3G16990
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	PROTEIN AT3G16990

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	HMH	2	Ligand/Ion	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	HMH	1	Ligand/Ion	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	HMH	1	Ligand/Ion	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:23 , HIS A:24	BINDING SITE FOR RESIDUE SO4 A 1403
2	AC2	SOFTWARE	ARG B:64 , ASP B:68 , ARG B:110 , VAL B:127 , LYS B:128 , TYR B:129 , HOH B:1466 , HOH B:1505	BINDING SITE FOR RESIDUE SO4 B 1401
3	AC3	SOFTWARE	ARG A:117 , GLU A:120 , HOH A:1597 , PHE B:118 , ASP B:121 , ARG B:205 , HOH B:1506	BINDING SITE FOR RESIDUE SO4 B 1402
4	AC4	SOFTWARE	ARG A:110 , VAL B:107 , SER B:192 , VAL B:195 , HOH B:1430 , HOH B:1563	BINDING SITE FOR RESIDUE SO4 B 1404
5	AC5	SOFTWARE	ASP A:47 , PHE A:50 , ILE A:139 , TYR A:143 , GLU A:210 , HOH A:1437	BINDING SITE FOR RESIDUE HMH A 1300
6	AC6	SOFTWARE	ASP B:47 , PHE B:50 , VAL B:51 , ILE B:139 , GLU B:140 , TYR B:143 , GLU B:210 , PHE B:213 , HOH B:1481	BINDING SITE FOR RESIDUE HMH B 1301

Asymmetric Unit

No.	Residues
1	A:150	-	A:165
2	B:150	-	B:165

(no "Cis Peptide Bond" information available for 2F2G)

(no "SAP(SNP)/Variant" information available for 2F2G)

(no "PROSITE Motif" information available for 2F2G)

(no "Exon" information available for 2F2G)

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
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Chain A from PDB  Type:PROTEIN  Length:215
 aligned with TENAE_ARATH | Q9ASY9 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:215
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214     
          TENAE_ARATH     5 GVIDTWIDKHRSIYTAATRHAFVVSIRDGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRACKDSGESSDMEVVLGGIASLNDEIEWFKREGSKWDVDFSTVVPQRANQEYGRFLEDLMSSEVKYPVIMTAFWAIEAVYQESFAHCLEDGNKTPVELTGACHRWGNDGFKQYCSSVKNIAERCLENASGEVLGEAEDVLVRVLELEVAFWEMSRG 219
               SCOP domains d2f2ga_ A: Seed maturation protein-related At3g16990                                                                                                                                                                    SCOP domains
               CATH domains 2f2gA00 A:5-219 Heme Oxygenase; Chain A                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh......eee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f2g A   5 GVIDTWIDKHRSIYTAATRHAFVVSIRDGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRACKDSGESSDmEVVLGGIASLNDEIEWFKREGSKWDVDFSTVVPQRANQEYGRFLEDLmSSEVKYPVImTAFWAIEAVYQESFAHCLEDGNKTPVELTGACHRWGNDGFKQYCSSVKNIAERCLENASGEVLGEAEDVLVRVLELEVAFWEmSRG 219
                                    14        24        34        44        54        64        74|       84        94       104       114       124       134       144       154       164       174       184       194       204       214 |   
                                                                                                 75-MSE                                         123-MSE   133-MSE                                                                            216-MSE

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with TENAE_ARATH | Q9ASY9 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:216
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      
          TENAE_ARATH     4 RGVIDTWIDKHRSIYTAATRHAFVVSIRDGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRACKDSGESSDMEVVLGGIASLNDEIEWFKREGSKWDVDFSTVVPQRANQEYGRFLEDLMSSEVKYPVIMTAFWAIEAVYQESFAHCLEDGNKTPVELTGACHRWGNDGFKQYCSSVKNIAERCLENASGEVLGEAEDVLVRVLELEVAFWEMSRG 219
               SCOP domains d2f2gb_ B: Seed maturation protein-related At3g16990                                                                                                                                                                     SCOP domains
               CATH domains 2f2gB00 B:4-219 Heme Oxygenase; Chain A                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..-----.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2f2g B   4 RGVIDTWIDKHRSIYTAATRHAFVVSIRDGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRACKDSGESSDmEVVLGGIASLNDEIEWFKREGSKWDVDFSTVVPQRANQEYGRFLEDLmSSEVKYPVImTAFWAIEAVYQESFAHC-----KTPVELTGACHRWGNDGFKQYCSSVKNIAERCLENASGEVLGEAEDVLVRVLELEVAFWEmSRG 219
                                    13        23        33        43        53        63        73 |      83        93       103       113       123       133       143      |  -  |    163       173       183       193       203       213  |   
                                                                                                  75-MSE                                         123-MSE   133-MSE          150   156                                                         216-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Heme oxygenase-like (107)

Superfamily: Heme oxygenase-like (107)

Family: TENA/THI-4 (15)

Protein domain: Seed maturation protein-related At3g16990 (1)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (1)

1a	d2f2ga_	A:
1b	d2f2gb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Heme Oxygenase; Chain A (84)

Homologous Superfamily: Heme Oxygenase; Chain A (84)

Thale cress (Arabidopsis thaliana) (2)

1a	2f2gA00	A:5-219
1b	2f2gB00	B:4-219

(no "Pfam Domain" information available for 2F2G)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TENAE_ARATH | Q9ASY9)

molecular function
	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:0050334	thiaminase activity	Catalysis of the reaction: H(2)O + thiamine = 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole + H(+).
biological process
	GO:0009228	thiamine biosynthetic process	The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
	GO:0009229	thiamine diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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SS Bonds (2, 2)

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