1RYD - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE FROM ZYMOMONAS MOBILIS

Authors :   Y. Kim, M. Arora, M. Straza, A. Joachimiak

Date :   22 Dec 03 (Deposition) - 15 Feb 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Oxidoreductase, Glucose, Fructose, Nadp, Zymomonas Mobilis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, M. Arora, M. Straza, A. Joachimiak
Crystal Structure Of Glucose-Fructose Oxidoreductase From Zymomonas Mobilis
To Be Published
PubMed: search

Molecule 1 - GLUCOSE-FRUCTOSE OXIDOREDUCTASE
	Chains	:	A, B
	EC Number	:	1.1.99.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ZYMOMONAS MOBILIS
	Organism Taxid	:	542

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	GLC	1	Ligand/Ion	ALPHA-D-GLUCOSE
4	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	ACT	6	Ligand/Ion	ACETATE ION
2	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
3	GLC	2	Ligand/Ion	ALPHA-D-GLUCOSE
4	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:236 , ILE A:254 , GLN A:256 , ALA B:235 , TYR B:236 , ILE B:254 , GLN B:256	BINDING SITE FOR RESIDUE GLC B 601
2	AC2	SOFTWARE	TYR B:21 , ASN B:193 , ARG B:354 , TRP B:373 , GLY B:374 , TYR B:375 , HOH B:706 , HOH B:708	BINDING SITE FOR RESIDUE ACT B 603
3	AC3	SOFTWARE	THR A:133 , GLY A:207 , GLN A:357 , TYR A:360	BINDING SITE FOR RESIDUE ACT A 604
4	AC4	SOFTWARE	MET A:319 , HOH A:740	BINDING SITE FOR RESIDUE ACT A 605
5	AC5	SOFTWARE	VAL A:10 , PRO A:11 , THR A:13 , PRO A:14 , ALA A:15 , GLY A:16 , ARG A:17 , LEU A:39 , GLY A:40 , LYS A:41 , TYR A:42 , SER A:64 , GLY A:65 , LYS A:69 , TYR A:87 , ILE A:105 , LEU A:106 , PRO A:107 , ASN A:108 , LEU A:110 , HIS A:111 , GLU A:128 , LYS A:129 , ARG A:157 , ALA A:196 , TRP A:199 , ARG A:200 , TYR A:217 , TYR A:296 , HOH A:739 , HOH A:766 , HOH A:779 , HOH A:822 , HOH A:853 , HOH A:859 , HOH A:866	BINDING SITE FOR RESIDUE NDP A 700
6	AC6	SOFTWARE	VAL B:10 , PRO B:11 , THR B:13 , PRO B:14 , ALA B:15 , GLY B:16 , ARG B:17 , GLY B:38 , LEU B:39 , GLY B:40 , LYS B:41 , TYR B:42 , SER B:64 , GLY B:65 , LYS B:69 , TYR B:87 , ILE B:105 , LEU B:106 , PRO B:107 , ASN B:108 , LEU B:110 , HIS B:111 , GLU B:128 , LYS B:129 , PRO B:130 , ARG B:157 , ALA B:196 , TRP B:199 , ARG B:200 , TYR B:217 , TYR B:296 , HOH B:711 , HOH B:734 , HOH B:846 , HOH B:854 , HOH B:883 , HOH B:892 , HOH B:918 , HOH B:1045	BINDING SITE FOR RESIDUE NDP B 701
7	AC7	SOFTWARE	PRO B:25 , MET B:26 , GLN B:55 , HOH B:853	BINDING SITE FOR RESIDUE BME B 602

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

Asymmetric Unit

No.	Residues
1	Lys A:129	-	Pro A:130
2	Asp A:291	-	Pro A:292
3	Lys B:129	-	Pro B:130
4	Asp B:291	-	Pro B:292

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

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

(no "Exon" information available for 1RYD)

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)
	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:381
 aligned with GFO_ZYMMO | Q07982 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:381
                                    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       342       352       362       372       382       392       402       412       422       432 
            GFO_ZYMMO    53 ATLPAGASQVPTTPAGRPMPYAIRPMPEDRRFGYAIVGLGKYALNQILPGFAGCQHSRIEALVSGNAEKAKIVAAEYGVDPRKIYDYSNFDKIAKDPKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQLGKLGMVTTDNSDVMDQNDPAQQWRLRRELAGGGSLMDIGIYGLNGTRYLLGEEPIEVRAYTYSDPNDERFVEVEDRIIWQMRFRSGALSHGASSYSTTTTSRFSVQGDKAVLLMDPATGYYQNLISVQTPGHANQSMMPQFIMPANNQFSAQLDHLAEAVINNKPVRSPGEEGMQDVRLIQAIYEAARTGRPVNTDWGYVRQGGY 433
               SCOP domains -----------------------------d1ryda1 A:30-160,A:323-381 Glucose-fructose oxidoreductase, N-terminal domain                                                      d1ryda2 A:161-322 Glucose-fructose oxidoreductase                                                                                                                 d1ryda1 A:30-160,A:323-381                                  SCOP domains
               CATH domains ---------------------1rydA01 A:22-160,A:317-345 NAD(P)-binding Rossmann-like Domain                                                                             1rydA02 A:161-316,A:346-381 Dihydrodipicolinate Reductase; domain 2                                                                                         1rydA01 A:22-160,A:317-345   1rydA02 A:161-316,A:346-381          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh......................eeeeee..hhhhhhh.hhhhh....eeeeeee..hhhhhhhhhhhhh.....ee...hhhhhhh.....eeee..hhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee......hhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeeee....hhhhh....eeeeeeee....eeeeeee.....eeeeeeee...eeee..........eeeee..eeeee..........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..ee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ryd A   1 ATLPAGASQVPTTPAGRPMPYAIRPMPEDRRFGYAIVGLGKYALNQILPGFAGCQHSRIEALVSGNAEKAKIVAAEYGVDPRKIYDYSNFDKIAKDPKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQLGKLGMVTTDNSDVMDQNDPAQQWRLRRELAGGGSLMDIGIYGLNGTRYLLGEEPIEVRAYTYSDPNDERFVEVEDRIIWQMRFRSGALSHGASSYSTTTTSRFSVQGDKAVLLMDPATGYYQNLISVQTPGHANQSMMPQFIMPANNQFSAQLDHLAEAVINNKPVRSPGEEGMQDVRLIQAIYEAARTGRPVNTDWGYVRQGGY 381
                                    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       330       340       350       360       370       380

Chain B from PDB  Type:PROTEIN  Length:381
 aligned with GFO_ZYMMO | Q07982 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:381
                                    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       342       352       362       372       382       392       402       412       422       432 
            GFO_ZYMMO    53 ATLPAGASQVPTTPAGRPMPYAIRPMPEDRRFGYAIVGLGKYALNQILPGFAGCQHSRIEALVSGNAEKAKIVAAEYGVDPRKIYDYSNFDKIAKDPKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQLGKLGMVTTDNSDVMDQNDPAQQWRLRRELAGGGSLMDIGIYGLNGTRYLLGEEPIEVRAYTYSDPNDERFVEVEDRIIWQMRFRSGALSHGASSYSTTTTSRFSVQGDKAVLLMDPATGYYQNLISVQTPGHANQSMMPQFIMPANNQFSAQLDHLAEAVINNKPVRSPGEEGMQDVRLIQAIYEAARTGRPVNTDWGYVRQGGY 433
               SCOP domains -----------------------------d1rydb1 B:30-160,B:323-381 Glucose-fructose oxidoreductase, N-terminal domain                                                      d1rydb2 B:161-322 Glucose-fructose oxidoreductase                                                                                                                 d1rydb1 B:30-160,B:323-381                                  SCOP domains
               CATH domains ---------------------1rydB01 B:22-160,B:317-345 NAD(P)-binding Rossmann-like Domain                                                                             1rydB02 B:161-316,B:346-381 Dihydrodipicolinate Reductase; domain 2                                                                                         1rydB01 B:22-160,B:317-345   1rydB02 B:161-316,B:346-381          CATH domains
           Pfam domains (1) -------------------------------GFO_IDH_MocA-1rydB01 B:32-156                                                                                                -----------GFO_IDH_MocA_C-1rydB03 B:168-282                                                                                   --------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------GFO_IDH_MocA-1rydB02 B:32-156                                                                                                -----------GFO_IDH_MocA_C-1rydB04 B:168-282                                                                                   --------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhh......................eeeeee..hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh..hhh.ee...hhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee......hhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeeee....hhhhh....eeeeeeee....eeeeeee.....eeeeeeee...eeee..........eeeee..eeeee..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ryd B   1 ATLPAGASQVPTTPAGRPMPYAIRPMPEDRRFGYAIVGLGKYALNQILPGFAGCQHSRIEALVSGNAEKAKIVAAEYGVDPRKIYDYSNFDKIAKDPKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQLGKLGMVTTDNSDVMDQNDPAQQWRLRRELAGGGSLMDIGIYGLNGTRYLLGEEPIEVRAYTYSDPNDERFVEVEDRIIWQMRFRSGALSHGASSYSTTTTSRFSVQGDKAVLLMDPATGYYQNLISVQTPGHANQSMMPQFIMPANNQFSAQLDHLAEAVINNKPVRSPGEEGMQDVRLIQAIYEAARTGRPVNTDWGYVRQGGY 381
                                    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       330       340       350       360       370       380

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Dihydrodipicolinate Reductase; domain 2 (182)

Homologous Superfamily: Dihydrodipicolinate Reductase; domain 2 (178)

Zymomonas mobilis. Organism_taxid: 542. (7)

1a	1rydA02	A:161-316,A:346-381
1b	1rydB02	B:161-316,B:346-381

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

Topology: Rossmann fold (7312)

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

Zymomonas mobilis. Organism_taxid: 542. (7)

2a	1rydA01	A:22-160,A:317-345
2b	1rydB01	B:22-160,B:317-345

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: GFO_IDH_MocA (25)

Zymomonas mobilis (3)

1a	GFO_IDH_MocA-1rydB01	B:32-156
1b	GFO_IDH_MocA-1rydB02	B:32-156

Clan: ox_reductase_C (19)

Family: GFO_IDH_MocA_C (19)

Zymomonas mobilis (3)

2a	GFO_IDH_MocA_C-1rydB03	B:168-282
2b	GFO_IDH_MocA_C-1rydB04	B:168-282

Asymmetric Unit(hide GO term definitions)

Chain A,B (GFO_ZYMMO | Q07982)

molecular function
	GO:0047061	glucose-fructose oxidoreductase activity	Catalysis of the reaction: D-fructose + D-glucose = D-glucitol + D-glucono-1,5-lactone.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006061	sorbitol biosynthetic process	The chemical reactions and pathways resulting in the formation of sorbitol (D-glucitol), one of the ten stereoisomeric hexitols. It can be derived from glucose by reduction of the aldehyde group.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asp A:291 - Pro A:292	[ RasMol ]
		Asp B:291 - Pro B:292	[ RasMol ]
		Lys A:129 - Pro A:130	[ RasMol ]
		Lys B:129 - Pro B:130	[ RasMol ]

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	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	1ryd
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	GFO_ZYMMO \| Q07982
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	1.1.99.28
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	GFO_ZYMMO \| Q07982
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	GFO_ZYMMO \| Q07982	:	1evj 1h6a 1h6b 1h6c 1h6d 1ofg 1rye

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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CATH Domains (2, 4)

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Gene Ontology (6, 6)

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