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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF MOLYBDENUM COFACTOR BIOSYNTHESIS (AQ_061) FROM AQUIFEX AEOLICUS VF5

Authors :   J. Jeyakanthan, S. P. Kanaujia, K. Sekar, Y. Agari, A. Ebihara, S. Kuram A. Shinkai, Y. Shiro, S. Yokoyama, Riken Structural Genomics/Prot Initiative (Rsgi)

Date :   29 Mar 10 (Deposition) - 19 Jan 11 (Release) - 19 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Molybdopterin, Mpt, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. P. Kanaujia, J. Jeyakanthan, A. Shinkai, S. Kuramitsu, S. Yokoyama K. Sekar
Crystal Structures, Dynamics And Functional Implications Of Molybdenum-Cofactor Biosynthesis Protein Moga From Two Thermophilic Organisms
Acta Crystallogr. , Sect. F V. 67 2 2011
PubMed-ID: 21206014 | Reference-DOI: 10.1107/S1744309110035037

Molecule 1 - MOLYBDENUM COFACTOR BIOSYNTHESIS MOG
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL-21 CONDON PLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MOG, AQ_061
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	224324
	Strain	:	VF5

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:135 , GLY A:136 , LYS A:137 , SER A:140 , HOH A:699	BINDING SITE FOR RESIDUE EDO A 179
2	AC2	SOFTWARE	ALA A:64 , ASP A:65 , ARG A:126 , GLY A:127 , SER A:128 , HOH A:355 , HOH A:467	BINDING SITE FOR RESIDUE EDO A 180
3	AC3	SOFTWARE	GLU A:91 , CYS A:94 , GLU A:95 , MET A:97 , HOH A:363	BINDING SITE FOR RESIDUE PEG A 181
4	AC4	SOFTWARE	PRO A:99 , GLY A:102 , GLU A:103 , ARG A:106 , GLN A:121 , THR A:122 , HOH A:209 , HOH A:392 , HOH A:441 , HOH A:674 , HOH A:740 , GLU B:103 , GLU C:103	BINDING SITE FOR RESIDUE PEG A 182
5	AC5	SOFTWARE	ASP C:24 , LYS C:28 , TYR C:46	BINDING SITE FOR RESIDUE EDO C 179
6	AC6	SOFTWARE	VAL C:93 , CYS C:94 , GLU C:95 , ARG C:126 , HOH C:686 , HOH C:728	BINDING SITE FOR RESIDUE EDO C 180
7	AC7	SOFTWARE	ALA C:81 , PRO C:82 , ARG C:83 , HOH C:306 , HOH C:423 , HOH C:462	BINDING SITE FOR RESIDUE EDO C 182

(no "SS Bond" information available for 3MCI)

(no "Cis Peptide Bond" information available for 3MCI)

(no "SAP(SNP)/Variant" information available for 3MCI)

(no "PROSITE Motif" information available for 3MCI)

(no "Exon" information available for 3MCI)

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:177
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
         O66472_AQUAE     2 SEKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPKK 178
               SCOP domains d3mcia_ A: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeehhhhhh....hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhh.hhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mci A   2 SEKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPKK 178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     
         O66472_AQUAE     3 EKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
               SCOP domains d3mcib_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..hhhhh...hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mci B   3 EKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain C from PDB  Type:PROTEIN  Length:175
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     
         O66472_AQUAE     3 EKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
               SCOP domains d3mcic_ C: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------MoCF_biosynth-3mciC01 C:9-154                                                                                                                     ----------------------- Pfam domains (1)
           Pfam domains (2) ------MoCF_biosynth-3mciC02 C:9-154                                                                                                                     ----------------------- Pfam domains (2)
           Pfam domains (3) ------MoCF_biosynth-3mciC03 C:9-154                                                                                                                     ----------------------- Pfam domains (3)
         Sec.struct. author ....eeeeeeehhhhhhh...hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mci C   3 EKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

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) (23833)

Fold: Molybdenum cofactor biosynthesis proteins (49)

Superfamily: Molybdenum cofactor biosynthesis proteins (49)

Family: MogA-like (20)

Protein domain: automated matches (3)

Aquifex aeolicus [TaxId: 224324] (3)

1a	d3mcia_	A:
1b	d3mcib_	B:
1c	d3mcic_	C:

(no "CATH Domain" information available for 3MCI)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: MoCF_biosynth] (31)

Family: MoCF_biosynth (31)

Aquifex aeolicus (4)

1a	MoCF_biosynth-3mciC01	C:9-154
1b	MoCF_biosynth-3mciC02	C:9-154
1c	MoCF_biosynth-3mciC03	C:9-154

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (O66472_AQUAE | O66472)

biological process
	GO:0006777	Mo-molybdopterin cofactor biosynthetic process	The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
	GO:0032324	molybdopterin cofactor biosynthetic process	The chemical reactions and pathways resulting in the formation of the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 8)

Sites (7, 7)

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