1U3F - JenaLib

Title :   STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A 5,10-METHENYLTETRAHYDROFOLATE SYNTHETASE FROM MYCOPLASMA PNEUMONIAE (GI: 13508087)

Authors :   S. Chen, A. F. Yakunin, M. Proudfoot, R. Kim, S. -H. Kim, Berkeley Structural Genomics Center (Bsgc)

Date :   21 Jul 04 (Deposition) - 07 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Mycoplasma Pneumoniae; 5, 10-Methenyltetrahydrofolate Synthetase; 5-Formyltetrahydrofolate Cyclo-Ligase; Mthfs; Atp Binding; Ligase; Structural Genomics; Bsgc Structure Funded By Nih; Protein Structure Initiative; Psi; Berkeley Structural Genomics Center, Psi, Protein Structure Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chen, D. H. Shin, R. Pufan, R. Kim, S. -H. Kim
Crystal Structure Of Methenyltetrahydrofolate Synthetase From Mycoplasma Pneumoniae (Gi: 13508087) At 2. 2 A Resolution
Proteins V. 56 839 2004
PubMed-ID: 15281135 | Reference-DOI: 10.1002/PROT.20214
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:115 , GLY A:117 , PHE A:118 , LYS A:120 , GLY A:121 , TYR A:122 , TYR A:123 , ADP A:201 , HOH A:608 , HOH A:774 , HOH A:844	BINDING SITE FOR RESIDUE PO4 A 301
2	AC2	SOFTWARE	ARG B:115 , PHE B:118 , GLY B:119 , GLY B:121 , TYR B:122 , TYR B:123 , ADP B:202 , HOH B:623 , HOH B:626 , HOH B:651	BINDING SITE FOR RESIDUE PO4 B 302
3	AC3	SOFTWARE	ARG A:115 , ASP A:124 , ASP A:154 , ADP A:201 , HOH A:612 , HOH A:773	BINDING SITE FOR RESIDUE MG A 401
4	AC4	SOFTWARE	LYS B:3 , ASP B:124 , ASP B:154 , ADP B:202 , HOH B:723	BINDING SITE FOR RESIDUE MG B 402
5	AC5	SOFTWARE	LYS A:3 , ARG A:7 , LEU A:116 , GLY A:117 , PHE A:118 , GLY A:119 , LYS A:120 , GLY A:121 , ASP A:124 , ARG A:125 , MET A:128 , TRP A:153 , ASP A:154 , PO4 A:301 , MG A:401 , HOH A:608 , HOH A:612 , HOH A:628	BINDING SITE FOR RESIDUE ADP A 201
6	AC6	SOFTWARE	ILE A:52 , LYS A:53 , LYS B:3 , ARG B:7 , LEU B:116 , GLY B:117 , PHE B:118 , GLY B:119 , LYS B:120 , GLY B:121 , ASP B:124 , ARG B:125 , TRP B:153 , ASP B:154 , PO4 B:302 , MG B:402 , HOH B:606 , HOH B:626	BINDING SITE FOR RESIDUE ADP B 202

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:164
 aligned with MTHFS_MYCPN | P75430 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
          MTHFS_MYCPN     1 MDKNALRKQILQKRMALSTIEKSHLDQKINQKLVAFLTPKPCIKTIALYEPIKNEVTFVDFFFEFLKINQIRAVYPKVISDTEIIFIDQETNTFEPNQIDCFLIPLVGFNKDNYRLGFGKGYYDRYLMQLTRQQPKIGIAYSFQKGDFLADPWDVQLDLIINDE 164
               SCOP domains d1u3fa_ A: 5,10-methenyltetrahydrofolate synthetase homolog MPN348                                                                                                   SCOP domains
               CATH domains 1u3fA00 A:1-164 NagB/RpiA/CoA transferase-like                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......eee...........hhhhhhhhhhh..eeeeeee.....eeee.....eehhhhh.eeee...ee.....ee....hhhhhhhhhh.....eeee.hhhhh.............eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u3f A   1 MDKNALRKQILQKRMALSTIEKSHLDQKINQKLVAFLTPKPCIKTIALYEPIKNEVTFVDFFFEFLKINQIRAVYPKVISDTEIIFIDQETNTFEPNQIDCFLIPLVGFNKDNYRLGFGKGYYDRYLMQLTRQQPKIGIAYSFQKGDFLADPWDVQLDLIINDE 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with MTHFS_MYCPN | P75430 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
          MTHFS_MYCPN     1 MDKNALRKQILQKRMALSTIEKSHLDQKINQKLVAFLTPKPCIKTIALYEPIKNEVTFVDFFFEFLKINQIRAVYPKVISDTEIIFIDQETNTFEPNQIDCFLIPLVGFNKDNYRLGFGKGYYDRYLMQLTRQQPKIGIAYSFQKGDFLADPWDVQLDLIINDE 164
               SCOP domains d1u3fb_ B: 5,10-methenyltetrahydrofolate synthetase homolog MPN348                                                                                                   SCOP domains
               CATH domains 1u3fB00 B:1-164 NagB/RpiA/CoA transferase-like                                                                                                                       CATH domains
           Pfam domains (1) --5-FTHF_cyc-lig-1u3fB01 B:3-163                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) --5-FTHF_cyc-lig-1u3fB02 B:3-163                                                                                                                                   - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee...........hhhhhhhhhhh..eeeeeee.....eeee.....eehhhhh.eeeee..ee.....ee....hhhhhhhh.......eeee.hhhhh.............eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u3f B   1 MDKNALRKQILQKRMALSTIEKSHLDQKINQKLVAFLTPKPCIKTIALYEPIKNEVTFVDFFFEFLKINQIRAVYPKVISDTEIIFIDQETNTFEPNQIDCFLIPLVGFNKDNYRLGFGKGYYDRYLMQLTRQQPKIGIAYSFQKGDFLADPWDVQLDLIINDE 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Legend:		→ Mismatch	(orange background)
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		→ 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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MTHFS_MYCPN | P75430)

molecular function
	GO:0030272	5-formyltetrahydrofolate cyclo-ligase activity	Catalysis of the reaction: 5-formyltetrahydrofolate + ATP = 5,10-methenyltetrahydrofolate + ADP + H(+) + phosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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