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Asym./Biol. Unit (Jmol Viewer)

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Title :   YGFZ PROTEIN

Authors :   A. Teplyakov, G. Obmolova, G. L. Gilliland, Structure 2 Function Project (S2F)

Date :   24 Jan 03 (Deposition) - 09 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A

Keywords :   Ygfz, Structural Genomics, Unknown Function, Structure 2 Function Project, S2F (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Teplyakov, G. Obmolova, E. Sarikaya, S. Pullalarevu, W. Krajewski, A. Galkin, A. J. Howard, O. Herzberg, G. L. Gilliland
Crystal Structure Of The Ygfz Protein From Escherichia Coli Suggests A Folate-Dependent Regulatory Role In One-Carbon Metabolism.
J. Bacteriol. V. 186 7134 2004
PubMed-ID: 15489424 | Reference-DOI: 10.1128/JB.186.21.7134-7140.2004
(for further references see the PDB file header)

Molecule 1 - YGFZ PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	YGFZ OR B2898
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	SPOT PR51

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:27 , ARG A:74 , PHE A:154 , LEU A:162 , TRP A:189 , ASN A:193 , HOH A:416	BINDING SITE FOR RESIDUE SO4 A 400
2	AC2	SOFTWARE	GLY A:79 , LYS A:145 , HOH A:497	BINDING SITE FOR RESIDUE SO4 A 401

(no "SS Bond" information available for 1NRK)

Asymmetric/Biological Unit

No.	Residues
1	His A:156	-	Pro A:157

(no "SAP(SNP)/Variant" information available for 1NRK)

(no "PROSITE Motif" information available for 1NRK)

(no "Exon" information available for 1NRK)

Asymmetric/Biological 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:325
 aligned with YGFZ_ECOLI | P0ADE8 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:325
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320     
           YGFZ_ECOLI     1 MAFTPFPPRQPTASARLPLTLMTLDDWALATITGADSEKYMQGQVTADVSQMAEDQHLLAAHCDAKGKMWSNLRLFRDGDGFAWIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQVVKEGATTLLWFEHPAERFLIVTDEATANMLTDKLRGEAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEMVARAKFRGANKRALWLLAGSASRLPEAGEDLELKMGENWRRTGTVLAAVKLEDGQVVVQVVMNNDMEPDSIFRVRDDANTLHIEPLPYSLE 325
               SCOP domains d1nrka2 A:1-243 Hypothetical protein YgfZ, N-terminal domain                                                                                                                                                                                       d1nrka1 A:244-325 Hypothetical protein YgfZ, C-terminal domain                     SCOP domains
               CATH domains --------------------------1nrkA02 A:27-113 Aminomethyltransferase beta-barrel domains                            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------GCV_T-1nrkA01 A:21-219                                                                                                                                                                                 ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh..eeee...eeeeeee..hhhhhhhh..............eeeeee.....eeeeeeeeee..eeeeeee..hhhhhhhhhhhhhhhh..eeeee...eeeeee..hhhhhhhh...........eeee..eeeeee.....eeeeeehhhhhhhhhhhhh...eeeehhhhhhhhhhh.....hhhhh...hhhhhhhhhhh..........hhhhhhhhhhh....eeeeeeeee.......................eeeeeee....eeeeeeeee..................eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nrk A   1 mAFTPFPPRQPTASARLPLTLmTLDDWALATITGADSEKYmQGQVTADVSQmAEDQHLLAAHCDAKGKmWSNLRLFRDGDGFAWIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQVVKEGATTLLWFEHPAERFLIVTDEATANmLTDKLRGEAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEmVARAKFRGANKRALWLLAGSASRLPEAGEDLELKmGENWRRTGTVLAAVKLEDGQVVVQVVmNNDmEPDSIFRVRDDANTLHIEPLPYSLE 325
                            |       10        20 |      30        40|       50 |      60        70        80        90       100       110       120       130       140       150       160       170 |     180       190       200       210       220       230   |   240       250       260       270       280       290     | 300       310       320     
                            |                   22-MSE             41-MSE     52-MSE           69-MSE                                                                                                172-MSE                                                       234-MSE                            269-MSE                    296-MSE                         
                            1-MSE                                                                                                                                                                                                                                                                                                    300-MSE

Chain A from PDB  Type:PROTEIN  Length:325
 aligned with YGFZ_SHIFL | P0ADE9 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:325
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320     
           YGFZ_SHIFL     1 MAFTPFPPRQPTASARLPLTLMTLDDWALATITGADSEKYMQGQVTADVSQMAEDQHLLAAHCDAKGKMWSNLRLFRDGDGFAWIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQVVKEGATTLLWFEHPAERFLIVTDEATANMLTDKLRGEAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEMVARAKFRGANKRALWLLAGSASRLPEAGEDLELKMGENWRRTGTVLAAVKLEDGQVVVQVVMNNDMEPDSIFRVRDDANTLHIEPLPYSLE 325
               SCOP domains d1nrka2 A:1-243 Hypothetical protein YgfZ, N-terminal domain                                                                                                                                                                                       d1nrka1 A:244-325 Hypothetical protein YgfZ, C-terminal domain                     SCOP domains
               CATH domains --------------------------1nrkA02 A:27-113 Aminomethyltransferase beta-barrel domains                            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------GCV_T-1nrkA01 A:21-219                                                                                                                                                                                 ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh..eeee...eeeeeee..hhhhhhhh..............eeeeee.....eeeeeeeeee..eeeeeee..hhhhhhhhhhhhhhhh..eeeee...eeeeee..hhhhhhhh...........eeee..eeeeee.....eeeeeehhhhhhhhhhhhh...eeeehhhhhhhhhhh.....hhhhh...hhhhhhhhhhh..........hhhhhhhhhhh....eeeeeeeee.......................eeeeeee....eeeeeeeee..................eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nrk A   1 mAFTPFPPRQPTASARLPLTLmTLDDWALATITGADSEKYmQGQVTADVSQmAEDQHLLAAHCDAKGKmWSNLRLFRDGDGFAWIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQVVKEGATTLLWFEHPAERFLIVTDEATANmLTDKLRGEAELNNSQQWLALNIEAGFPVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEmVARAKFRGANKRALWLLAGSASRLPEAGEDLELKmGENWRRTGTVLAAVKLEDGQVVVQVVmNNDmEPDSIFRVRDDANTLHIEPLPYSLE 325
                            |       10        20 |      30        40|       50 |      60        70        80        90       100       110       120       130       140       150       160       170 |     180       190       200       210       220       230   |   240       250       260       270       280       290     | 300       310       320     
                            1-MSE               22-MSE             41-MSE     52-MSE           69-MSE                                                                                                172-MSE                                                       234-MSE                            269-MSE                    296-MSE                         
                                                                                                                                                                                                                                                                                                                                     300-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: Aminomethyltransferase beta-barrel domains (3)

Escherichia coli. Organism_taxid: 562. (2)

1nrkA02

A:27-113

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FBD (14)

Family: GCV_T (12)

Escherichia coli (strain K12) (3)

GCV_T-1nrkA01

A:21-219

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (YGFZ_SHIFL | P0ADE9)

molecular function
	GO:0005542	folic acid binding	Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
biological process
	GO:0009451	RNA modification	The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A (YGFZ_ECOLI | P0ADE8)

molecular function
	GO:0005542	folic acid binding	Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
biological process
	GO:0009451	RNA modification	The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
	GO:0016226	iron-sulfur cluster assembly	The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		His A:156 - Pro A:157	[ RasMol ]

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	YGFZ_ECOLI \| P0ADE8	:	1vly
	YGFZ_SHIFL \| P0ADE9	:	1vly

Description

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