2Z95 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF GDP-D-MANNOSE DEHYDRATASE FROM AQUIFEX AEOLICUS VF5

Authors :   H. Niwa, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   18 Sep 07 (Deposition) - 18 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

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

Reference :   H. Niwa, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Gdp-D-Mannose Dehydratase From Aquifex Aeolicus Vf5
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GDP-D-MANNOSE DEHYDRATASE
	Chains	:	A, B, C, D
	EC Number	:	4.2.1.47
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RFBD
	Organism Scientific	:	AQUIFEX AEOLICUS VF5
	Organism Taxid	:	224324
	Strain	:	VF5

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:10 , ARG A:12 , GLY A:13 , GLN A:14 , ASP A:15 , ARG A:35 , ASP A:60 , LEU A:61 , LEU A:82 , ALA A:83 , ALA A:84 , SER A:86 , SER A:126 , THR A:127 , TYR A:151 , LYS A:155 , LEU A:178 , ASN A:180 , HIS A:181 , ARG A:186 , HOH A:1031 , HOH A:1043 , HOH A:1060 , HOH A:1074	BINDING SITE FOR RESIDUE NDP A 1001
2	AC2	SOFTWARE	GLU D:129 , ASN D:180 , GLU D:189 , PHE D:190 , LYS D:194 , GLY D:213 , ASN D:214 , ALA D:217 , ARG D:219 , ARG D:297 , GLU D:300	BINDING SITE FOR RESIDUE GDP D 1002

(no "SS Bond" information available for 2Z95)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:137	-	Pro A:138
2	Ile B:137	-	Pro B:138
3	Ile C:137	-	Pro C:138
4	Ile D:137	-	Pro D:138

(no "SAP(SNP)/Variant" information available for 2Z95)

(no "PROSITE Motif" information available for 2Z95)

(no "Exon" information available for 2Z95)

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:333
 aligned with O67175_AQUAE | O67175 from UniProtKB/TrEMBL  Length:345

    Alignment length:338
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
         O67175_AQUAE     3 GKRALITGIRGQDGAYLAKLLLEKGYEVYGADRRSGEFASWRLKELGIENDVKIIHMDLLEFSNIIRTIEKVQPDEVYNLAAQSFVGVSFEQPILTAEVDAIGVLRILEALRTVKPDTKFYQASTSEMFGKVQEIPQTEKTPFYPRSPYAVAKLFGHWITVNYREAYNMFACSGILFNHESPLRGIEFVTRKITYSLARIKYGLQDKLVLGNLNAKRDWGYAPEYVEAMWLMMQQPEPDDYVIATGETHTVREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIVEVSEEFFRPAEVDILVGNPEKAMKKLGWKPRTTFDELVEIMMEADLKRVRD 340
               SCOP domains d2z95a_ A: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2z95A01 A:3-186,A:222-249,A:301-3     21 NAD(P)-binding Rossmann-like Domain                                                                                                            2z95A02                            2z95A01                     2z95A02 A:187-221,A:250-300,A:322-340              2z95A01              2z95A02             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee.-----.hhhhhhh.....eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..ee.......hhhhhhhhhhhhhh......eee.....ee..eehhhhhhhhhhhhh.....eeee.....eehhhhhhhhhhhh...eeee.hhhh.eeee.....eeeee................hhhhhhhh......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z95 A   3 GKRALITGIRGQDGAYLAKLLLEKGYEVYGADR-----ASWRLKELGIENDVKIIHMDLLEFSNIIRTIEKVQPDEVYNLAAQSFVGVSFEQPILTAEVDAIGVLRILEALRTVKPDTKFYQASTSEMFGKVQEIPQTEKTPFYPRSPYAVAKLFGHWITVNYREAYNMFACSGILFNHESPLRGIEFVTRKITYSLARIKYGLQDKLVLGNLNAKRDWGYAPEYVEAMWLMMQQPEPDDYVIATGETHTVREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIVEVSEEFFRPAEVDILVGNPEKAMKKLGWKPRTTFDELVEIMMEADLKRVRD 340
                                    12        22        32  |     42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
                                                           35    41

Chain B from PDB  Type:PROTEIN  Length:332
 aligned with O67175_AQUAE | O67175 from UniProtKB/TrEMBL  Length:345

    Alignment length:338
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
         O67175_AQUAE     3 GKRALITGIRGQDGAYLAKLLLEKGYEVYGADRRSGEFASWRLKELGIENDVKIIHMDLLEFSNIIRTIEKVQPDEVYNLAAQSFVGVSFEQPILTAEVDAIGVLRILEALRTVKPDTKFYQASTSEMFGKVQEIPQTEKTPFYPRSPYAVAKLFGHWITVNYREAYNMFACSGILFNHESPLRGIEFVTRKITYSLARIKYGLQDKLVLGNLNAKRDWGYAPEYVEAMWLMMQQPEPDDYVIATGETHTVREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIVEVSEEFFRPAEVDILVGNPEKAMKKLGWKPRTTFDELVEIMMEADLKRVRD 340
               SCOP domains d2z95b_ B: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2z95B01 B:3-186,B:222-249,B:301-      321 NAD(P)-binding Rossmann-like Domain                                                                                                           2z95B02                            2z95B01                     2z95B02 B:187-221,B:250-300,B:322-340              2z95B01              2z95B02             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee------.hhhhhhh......eeee.....hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....ee..eehhhhhhhhhhhhhh....eeee.....eehhhhhhhhhhhh...eeee.hhhh.eeee....eeeeee................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z95 B   3 GKRALITGIRGQDGAYLAKLLLEKGYEVYGAD------ASWRLKELGIENDVKIIHMDLLEFSNIIRTIEKVQPDEVYNLAAQSFVGVSFEQPILTAEVDAIGVLRILEALRTVKPDTKFYQASTSEMFGKVQEIPQTEKTPFYPRSPYAVAKLFGHWITVNYREAYNMFACSGILFNHESPLRGIEFVTRKITYSLARIKYGLQDKLVLGNLNAKRDWGYAPEYVEAMWLMMQQPEPDDYVIATGETHTVREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIVEVSEEFFRPAEVDILVGNPEKAMKKLGWKPRTTFDELVEIMMEADLKRVRD 340
                                    12        22        32 |      42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
                                                          34     41

Chain C from PDB  Type:PROTEIN  Length:338
 aligned with O67175_AQUAE | O67175 from UniProtKB/TrEMBL  Length:345

    Alignment length:338
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
         O67175_AQUAE     3 GKRALITGIRGQDGAYLAKLLLEKGYEVYGADRRSGEFASWRLKELGIENDVKIIHMDLLEFSNIIRTIEKVQPDEVYNLAAQSFVGVSFEQPILTAEVDAIGVLRILEALRTVKPDTKFYQASTSEMFGKVQEIPQTEKTPFYPRSPYAVAKLFGHWITVNYREAYNMFACSGILFNHESPLRGIEFVTRKITYSLARIKYGLQDKLVLGNLNAKRDWGYAPEYVEAMWLMMQQPEPDDYVIATGETHTVREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIVEVSEEFFRPAEVDILVGNPEKAMKKLGWKPRTTFDELVEIMMEADLKRVRD 340
               SCOP domains d2z95c_ C: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2z95C01 C:3-186,C:222-249,C:301-321 NAD(P)-binding Rossmann-like Domain                                                                                                                 2z95C02                            2z95C01                     2z95C02 C:187-221,C:250-300,C:322-340              2z95C01              2z95C02             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeee........hhhhhh..hhh.eee......hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh.................hhhhhhhhhhhhhhhhhhhhh...eeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....ee..eehhhhhhhhhhhhh.....eeee.....eehhhhhhhhhhhh...eeee.hhhh.eeee.....eeeee................hhhhhhhh......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z95 C   3 GKRALITGIRGQDGAYLAKLLLEKGYEVYGADRRSGEFASWRLKELGIENDVKIIHMDLLEFSNIIRTIEKVQPDEVYNLAAQSFVGVSFEQPILTAEVDAIGVLRILEALRTVKPDTKFYQASTSEMFGKVQEIPQTEKTPFYPRSPYAVAKLFGHWITVNYREAYNMFACSGILFNHESPLRGIEFVTRKITYSLARIKYGLQDKLVLGNLNAKRDWGYAPEYVEAMWLMMQQPEPDDYVIATGETHTVREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIVEVSEEFFRPAEVDILVGNPEKAMKKLGWKPRTTFDELVEIMMEADLKRVRD 340
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332

Chain D from PDB  Type:PROTEIN  Length:332
 aligned with O67175_AQUAE | O67175 from UniProtKB/TrEMBL  Length:345

    Alignment length:335
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     
         O67175_AQUAE     3 GKRALITGIRGQDGAYLAKLLLEKGYEVYGADRRSGEFASWRLKELGIENDVKIIHMDLLEFSNIIRTIEKVQPDEVYNLAAQSFVGVSFEQPILTAEVDAIGVLRILEALRTVKPDTKFYQASTSEMFGKVQEIPQTEKTPFYPRSPYAVAKLFGHWITVNYREAYNMFACSGILFNHESPLRGIEFVTRKITYSLARIKYGLQDKLVLGNLNAKRDWGYAPEYVEAMWLMMQQPEPDDYVIATGETHTVREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIVEVSEEFFRPAEVDILVGNPEKAMKKLGWKPRTTFDELVEIMMEADLKR 337
               SCOP domains d2z95d_ D: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2z95D01 D:3-186,D:222-249,D:301-   321 NAD(P)-binding Rossmann-like Domain                                                                                                              2z95D02                            2z95D01                     2z95D02 D:187-221,D:250-300,D:322-337              2z95D01              2z95D02          CATH domains
           Pfam domains (1) ---Epimerase-2z95D01 D:6-246                                                                                                                                                                                                                        ------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---Epimerase-2z95D02 D:6-246                                                                                                                                                                                                                        ------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---Epimerase-2z95D03 D:6-246                                                                                                                                                                                                                        ------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---Epimerase-2z95D04 D:6-246                                                                                                                                                                                                                        ------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeee.---....hhhhhhh.....eeee.....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhh....eeeeee..ee.......hhhhhhhhhhhhhh......eee.....eee.eehhhhhhhhhhhhh......eee....eeehhhhhhhhhhh......ee......eee......eeeee.hhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z95 D   3 GKRALITGIRGQDGAYLAKLLLEKGYEVYGAD---GEFASWRLKELGIENDVKIIHMDLLEFSNIIRTIEKVQPDEVYNLAAQSFVGVSFEQPILTAEVDAIGVLRILEALRTVKPDTKFYQASTSEMFGKVQEIPQTEKTPFYPRSPYAVAKLFGHWITVNYREAYNMFACSGILFNHESPLRGIEFVTRKITYSLARIKYGLQDKLVLGNLNAKRDWGYAPEYVEAMWLMMQQPEPDDYVIATGETHTVREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIVEVSEEFFRPAEVDILVGNPEKAMKKLGWKPRTTFDELVEIMMEADLKR 337
                                    12        22        32 |   |  42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     
                                                          34  38

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: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: automated matches (114)

Aquifex aeolicus [TaxId: 224324] (2)

1a	d2z95a_	A:
1b	d2z95b_	B:
1c	d2z95c_	C:
1d	d2z95d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Aquifex aeolicus vf5. Organism_taxid: 224324. Strain: vf5. (5)

1a	2z95B01	B:3-186,B:222-249,B:301-321
1b	2z95D01	D:3-186,D:222-249,D:301-321
1c	2z95C01	C:3-186,C:222-249,C:301-321
1d	2z95A01	A:3-186,A:222-249,A:301-321

Architecture: Alpha-Beta Complex (3881)

Topology: UDP-galactose 4-epimerase; domain 1 (99)

Homologous Superfamily: UDP-galactose 4-epimerase, domain 1 (99)

Aquifex aeolicus vf5. Organism_taxid: 224324. Strain: vf5. (2)

2a	2z95A02	A:187-221,A:250-300,A:322-340
2b	2z95B02	B:187-221,B:250-300,B:322-340
2c	2z95C02	C:187-221,C:250-300,C:322-340
2d	2z95D02	D:187-221,D:250-300,D:322-337

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Epimerase (42)

Aquifex aeolicus (2)

1a	Epimerase-2z95D01	D:6-246
1b	Epimerase-2z95D02	D:6-246
1c	Epimerase-2z95D03	D:6-246
1d	Epimerase-2z95D04	D:6-246

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (O67175_AQUAE | O67175)

molecular function
	GO:0008446	GDP-mannose 4,6-dehydratase activity	Catalysis of the reaction: GDP-alpha-D-mannose = GDP-4-dehydro-6-deoxy-alpha-D-mannose + H(2)O.
	GO:0070401	NADP+ binding	Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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.
biological process
	GO:0019673	GDP-mannose metabolic process	The chemical reactions and pathways involving GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.

Asymmetric/Biological Unit
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		Ile C:137 - Pro C:138	[ RasMol ]
		Ile D:137 - Pro D:138	[ RasMol ]

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	2z95
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	O67175_AQUAE \| O67175
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	4.2.1.47
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	O67175_AQUAE \| O67175	:	2z1m

(no "Related Entries Specified in the PDB File" available for 2Z95)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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