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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   X-RAY STRUCTURE OF THE ARCHAEOGLOBUS FULGIDUS METHENYL-TETRAHYDROMETHANOPTERIN CYCLOHYDROLASE IN COMPLEX WITH TETRAHYDROMETHANPTERIN

Authors :   V. Upadhyay, U. Demmer, E. Warkentin, J. Moll, S. Shima, U. Ermler

Date :   31 Aug 12 (Deposition) - 31 Oct 12 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Tetrahydromethanopterin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Upadhyay, U. Demmer, E. Warkentin, J. Moll, S. Shima, U. Ermler
Structure And Catalytic Mechanism Of N(5), N(10)-Methenyl-Tetrahydromethanopterin Cyclohydrolase.
Biochemistry V. 51 8435 2012
PubMed-ID: 23013430 | Reference-DOI: 10.1021/BI300777K

Molecule 1 - METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE
	Chains	:	A, B, C
	EC Number	:	3.5.4.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-24A(+)
	Expression System Strain	:	ROSETTA (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AF_1935, MCH
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	224325
	Strain	:	DSM 4304
	Synonym	:	METHENYL-H4MPT CYCLOHYDROLASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	N4M	2	Ligand/Ion	1-[4-({(1R)-1-[(6S,7S)-2-AMINO-7-METHYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]ETHYL}AMINO)PHENYL]-1-DEOXY-5-O-{5-O-[(R)-{[(1R)-1,3-DICARBOXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]-ALPHA-D-RIBOFURANOSYL}-D-XYLITOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:94 , ALA A:95 , GLY A:96 , MET A:107 , GLU A:140 , ILE A:180 , ARG A:183 , GLU A:186 , THR A:187 , MET A:222 , ASN A:226 , MET A:229 , PHE A:272 , PHE A:280 , HOH A:807	BINDING SITE FOR RESIDUE N4M A 401
2	AC2	SOFTWARE	LYS B:94 , ALA B:95 , GLY B:96 , MET B:107 , GLU B:140 , ILE B:180 , ARG B:183 , GLU B:186 , THR B:187 , MET B:222 , ASN B:226 , MET B:229 , PHE B:272 , PHE B:280 , HOH B:556	BINDING SITE FOR RESIDUE N4M B 401

(no "SS Bond" information available for 4GVQ)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:118	-	Pro A:119
2	Lys B:118	-	Pro B:119
3	Lys C:118	-	Pro C:119

(no "SAP(SNP)/Variant" information available for 4GVQ)

(no "PROSITE Motif" information available for 4GVQ)

(no "Exon" information available for 4GVQ)

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:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gvqa_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.eeee.....eeee.......hhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee.hhhhhhh......eeeee..eeeeee..hhhhhh.hhhhhhhhh.......eeeeee.....hhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee......hhhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhh...eeeeee.....eeeee..hhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvq A   1 MLSVNEIAAEIVEDMLDYEEELRIESKKLENGAIVVDCGVNVPGSYDAGIMYTQVCMGGLADVDIVVDTINDVPFAFVTEYTDHPAIACLGSQKAGWQIKVDKYFAMGSGPARALALKPKKTYERIEYEDDADVAVIALEANQLPDEKVMEFIAKECDVDPENVYALVAPTASIVGSVQISGRIVETAIFKMNEIGYDPKLIVSGAGRCPISPILENDLKAMGSTNDSMMYYGSVFLTVKKYDEILKNVPSCTSRDYGKPFYEIFKAANYDFYKIDPNLFAPAQIAVNDLETGKTYVHGKLNAEVLFQSYQIVLE 315
                                    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

Chain B from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gvqb_ B: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.eeee.....eeee.......hhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee.hhhhhhh......eeeee..eeeeee..hhhhhh.hhhhhhhhh.......eeeeee.....hhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee......hhhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhh...eeeeee.....eeeee..hhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvq B   1 MLSVNEIAAEIVEDMLDYEEELRIESKKLENGAIVVDCGVNVPGSYDAGIMYTQVCMGGLADVDIVVDTINDVPFAFVTEYTDHPAIACLGSQKAGWQIKVDKYFAMGSGPARALALKPKKTYERIEYEDDADVAVIALEANQLPDEKVMEFIAKECDVDPENVYALVAPTASIVGSVQISGRIVETAIFKMNEIGYDPKLIVSGAGRCPISPILENDLKAMGSTNDSMMYYGSVFLTVKKYDEILKNVPSCTSRDYGKPFYEIFKAANYDFYKIDPNLFAPAQIAVNDLETGKTYVHGKLNAEVLFQSYQIVLE 315
                                    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

Chain C from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gvqc_ C: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.eeee.....eeee.......hhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee.hhhhhhh......eeeee..eeeeee..hhhhhh.hhhhhhhhh.......eeeeee.....hhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeee......hhhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhh...eeeeee.....eeeee..hhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvq C   1 MLSVNEIAAEIVEDMLDYEEELRIESKKLENGAIVVDCGVNVPGSYDAGIMYTQVCMGGLADVDIVVDTINDVPFAFVTEYTDHPAIACLGSQKAGWQIKVDKYFAMGSGPARALALKPKKTYERIEYEDDADVAVIALEANQLPDEKVMEFIAKECDVDPENVYALVAPTASIVGSVQISGRIVETAIFKMNEIGYDPKLIVSGAGRCPISPILENDLKAMGSTNDSMMYYGSVFLTVKKYDEILKNVPSCTSRDYGKPFYEIFKAANYDFYKIDPNLFAPAQIAVNDLETGKTYVHGKLNAEVLFQSYQIVLE 315
                                    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

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Methenyltetrahydromethanopterin cyclohydrolase (5)

Superfamily: Methenyltetrahydromethanopterin cyclohydrolase (5)

Family: automated matches (4)

Protein domain: automated matches (4)

Archaeoglobus fulgidus [TaxId: 224325] (3)

1a	d4gvqa_	A:
1b	d4gvqb_	B:
1c	d4gvqc_	C:

(no "CATH Domain" information available for 4GVQ)

(no "Pfam Domain" information available for 4GVQ)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:118 - Pro A:119	[ RasMol ]
		Lys B:118 - Pro B:119	[ RasMol ]
		Lys C:118 - Pro C:119	[ RasMol ]

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (5, 5)

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